Compositions comprising thienopyrimidine and thienopyridine compounds and methods of use thereof

ABSTRACT

The present invention relates generally to thienopyrimidine and thienopyridine class compounds and methods of use thereof. In particular embodiments, the present invention provides compositions comprising thienopyrimidine class compounds and methods of use to inhibit the interaction of menin with MLL1, MLL2 and MLL-fusion oncoproteins (e.g., for the treatment of leukemia, solid cancers and other diseases dependent on activity of MLL1 and MLL2 or menin).

The present application claims priority to U.S. Provisional PatentApplication Ser. No. 61/780,099, filed Mar. 13, 2013, the entiredisclosure of which is herein incorporated by reference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under R01 CA160467-01awarded by the National Institutes of Health. The government has certainrights in the invention.

FIELD OF THE INVENTION

The present invention relates generally to thienopyrimidine andthienopyridine class compounds and methods of use thereof. In particularembodiments, the present invention provides compositions comprisingthienopyrimidine and thienopyridine class compounds and methods of useto inhibit the interaction of menin with MLL1, MLL2 and MLL-fusiononcoproteins (e.g., for the treatment of leukemia, solid cancers andother diseases dependent on activity of MLL1 and MLL2 or menin).

BACKGROUND OF THE INVENTION

Chromosomal translocations that affect the proto-oncogene Mixed LineageLeukemia (MLL) occur in aggressive human acute leukemias, both inchildren and adults (Sorensen et al., J Clin Invest., 1994. 93(1): p.429-37, Cox, et al., Am J Clin Pathol., 2004. 122(2): p. 298-306, hereinincorporated by reference in their entireties). They are particularlycommon in infants with acute myeloblastic leukemia (AML) and acutelymphoblastic leukemia (ALL) and constitute up to 80% of all infantacute leukemia cases. Fusion of MLL with one of 60 partner genes forms achimeric oncogene which upregulates HOX genes resulting in a blockage ofblood cell differentiation that ultimately leads to acute leukemia(Eguchi et al. Int J Hematol., 2003. 78(5): p. 390-401, hereinincorporated by reference in its entirety). Patients with leukemiasharboring MLL translocations have a very poor prognosis (35% five yearsurvival) and it is clear that novel therapeutic strategies are urgentlyneeded to treat these leukemias (Slany. Hematol Oncol., 2005. 23(1): p.1-9, herein incorporated by reference in its entirety). Menin is acritical cofactor in MLL-associated leukemias. Menin is atumor-suppressor protein encoded by the Multiple Endocrine Neoplasia(MEN) gene. Menin is a ubiquitously expressed nuclear protein that isengaged in interactions with a cohort of transcription factors,chromatin modifying proteins, and DNA processing and repair proteins(Agarwal et al. Horm Metab Res., 2005. 37(6): p. 369-74, hereinincorporated by reference in its entirety). The biological function ofmenin remains unclear and is context dependent. It functions as a tumorsuppressor in endocrine organs (Marx. Nat Rev Cancer., 2005. 5(5): p.367-75, herein incorporated by reference in its entirety) but has anoncogenic role in myeloid cells (Yokoyama et al., Cell., 2005. 123(2):p. 207-18, herein incorporated by reference in its entirety).Association of menin with oncogenic MLL fusion proteins constitutivelyup-regulates expression of HOX genes and impairs proliferation anddifferentiation of hematopoietic cells leading to leukemia development.Myeloid cells transformed with oncogenic MLL-AF9 fusion protein requiremenin for efficient proliferation (Chen et al., Proc Natl Acad Sci USA.,2006. 103(4): p. 1018-23, herein incorporated by reference in itsentirety). Menin is also required to maintain oncogenic transformationinduced by other MLL translocations, including MLL-ENL, MLL-GAS7 andMLL-AF6 (Yokoyama et al., Cell., 2005. 123(2): p. 207-18, hereinincorporated by reference in its entirety), demonstrating that meninfunctions as a general oncogenic cofactor in MLL-related leukemias andimplies the interaction of menin with MLL fusions and MLL is a valuabletarget for molecular therapy. The leukemogenic activity of MLL fusiononcoproteins is dependent on association with menin. Therefore,selective targeting of this interaction could provide an attractivetherapeutic approach to develop novel drugs for leukemias withtranslocations of MLL gene and other leukemias with upregulation of HOXgenes.

SUMMARY OF THE INVENTION

In some embodiments, the present invention provides compositions for thetreatment of leukemia which inhibit binding of one or more MLL fusionproteins to menin and/or MLL wild type to menin. In some embodiments,the composition comprises a thienopyrimidine and thienopyridine classcompounds.

In some embodiments, the thienopyrimidine and thienopyridine classcompound is of the general formula:

, wherein X, Y, W, R1, R2, R3, and R4 are independently selected fromany of the respective substituents described herein or depicted in anyof Tables 1-8, in any combination. For example, in some embodiments,R₁-R₄ each independently consist of or comprise: H, alkyl group (e.g.,straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane,hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane,3-methyl, 2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane,cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branchedcyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane,propylcyclohexane, etc.)), a substituted alkyl group (e.g.,halogen-substituted alkyl group (e.g., mono-, di-, tetra-, penta- andtrihaloethane (e.g., trifluoroethane), halomethane (e.g.,fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane(e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol,etc.), alkylamine (e.g., primary amine (e.g., ethylamine,iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine,iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondaryamines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.),tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thiolkyl,combinations thereof, etc.), a substituted cycloalkyl group (e.g.,halogen-substituted cycloalkyl group, alkyl-substituted cycloalkylgroup, cycloalkoxy group, cyclolkylamine, etc.), a halogen (e.g., F, Cl,Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring (e.g.,heteroaryl), a substituted aromatic ring (e.g., branched aromatic ring(e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g.,chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring(e.g., comprising one or more nitrogen, oxygen and/or sulfur memberswhich may be non-substituted or substituted with alkyl, aryl, halogen,hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring(e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfurmembers), carbocyclic or heterocyclic aromatic ring comprising carbonatoms and one or more nitrogen, oxygen and/or sulfur members fused toanother aromatic ring (e.g., heteroaryl), a multi-ring system comprisinga combination of elements selected from aromatic rings, cycloalkane,heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/orhalogen-containing substituents (e.g., substituted heteroaryl), or ahydrogen bond donor or a hydrogen bond acceptor, and/or combinationsthereof.

In some embodiments, the thienopyrimidine and thienopyridine classcompound is of a general formula of:

wherein R1 and R2 both independently comprise or consists of: H, alkylgroup (e.g., straight-chain alkyl (e.g., methane, ethane, propane,butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane,2-methyl-hexane, 3-methyl, 2-propyl-octane, etc.), cycloalkyl (e.g.,cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane,etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane,propylcyclohexane, etc.)), a substituted alkyl group (e.g.,halogen-substituted alkyl group (e.g., mono-, di-, tetra-, penta- andtrihaloethane (e.g., trifluoroethane), halomethane (e.g.,fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane(e.g., trifluoromethane), 1-trihalo, 2-halo-ethane, trihalobutane,etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g.,primary amine (e.g., ethylamine, iso-butylamine, n-propylamine,sec-butylamine, iso-propylamine, iso-amylamine, methylamine,dimethylamine, n-amylamine, etc.), secondary amines (e.g.,dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine(e.g., trimethylamine, triphenylamine, etc.), thiolkyl, combinationsthereof, etc.), a substituted cycloalkyl group (e.g.,halogen-substituted cycloalkyl group, alkyl-substituted cycloalkylgroup, cycloalkoxy group, cyclolkylamine, etc.), a halogen (e.g., F, Cl,Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring (e.g.,heteroaryl), a substituted aromatic ring (e.g., branched aromatic ring(e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g.,chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring(e.g., comprising one or more nitrogen, oxygen and/or sulfur memberswhich may be non-substituted or substituted with alkyl, aryl, halogen,hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring(e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfurmembers), carbocyclic or heterocyclic aromatic ring comprising carbonatoms and one or more nitrogen, oxygen and/or sulfur members fused toanother aromatic ring (e.g., heteroaryl), a multi-ring system comprisinga combination of elements selected from aromatic rings, cycloalkane,heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/orhalogen-containing substituents (e.g., substituted heteroaryl), or ahydrogen bond donor or a hydrogen bond acceptor, and/or combinationsthereof; and wherein A, B, and D each independently comprise or consistof: C, N, O, or S; wherein when one or more of A, B, and/or D comprise Oor S, there is no further substitution at that respective position;wherein when one or more of A, B, and/or D comprise N or C thatrespective position is optionally substituted, wherein the substituentat that respective position comprises or consists of: alkyl group (e.g.,straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane,hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane,3-methyl, 2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane,cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branchedcyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane,propylcyclohexane, etc.)), a substituted alkyl group (e.g.,halogen-substituted alkyl group (e.g., trihaloethane (e.g.,trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane(e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.),alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primaryamine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine,iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine,etc.), secondary amines (e.g., dimethylamine, methylethanolamine,diphenylamine, etc.), tertiary amine (e.g., trimethylamine,triphenylamine, etc.), thiolkyl, combinations thereof, etc.), asubstituted cycloalkyl group (e.g., halogen-substituted cycloalkylgroup, cycloalkoxy group, acyclolkylamine, etc.), a halogen (e.g., F,Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, asubstituted aromatic ring (e.g., branched aromatic ring (e.g.,ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene,fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprisingone or more nitrogen, oxygen and/or sulfur members which may benon-substituted or substituted with alkyl, aryl, halogen, hydrogen bonddonor or acceptor, a heterocyclic non-aromatic ring (e.g., comprisingcarbon and one or more nitrogen, oxygen and/or sulfur members),carbocyclic or heterocyclic aromatic ring (e.g., heteroaryl) comprisingcarbon atoms and one or more nitrogen, oxygen and/or sulfur membersfused to another aromatic ring, a multi-ring system comprising acombination of elements selected from aromatic rings (e.g., heteroaryl),cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-,S-, and/or halogen-containing substituents, or a hydrogen bond donor ora hydrogen bond acceptor, and/or combinations thereof; and wherein Y isN or C, and wherein when Y is C the Y position may be substituted withR^(a), with R^(a) consisting of or comprising an H, alkyl (e.g.,branched (e.g., isopropyl), straight chain (e.g., propyl), cycloalkyl(e.g., cyclopropyl)), heteroalkyl (e.g., methyl propyl ether),alkyl-substituted aryl (e.g., ethylbenzene), substituted alkyl (e.g.,halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethylgroup), monohaloalkyl group (e.g. monofluoroethyl group), dihaloalkylgroup (e.g. difluoroethyl group), trihaloethyl group (e.g.,trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl ((CH₂)₂CF₃),trihalobutyl group (e.g., trifluorobutyl group ((CH₂)₃CF₃)),1-trifluoro, 2-ethanol, alcohol (e.g., (CH₂)_(n)OH, wherein n=0-10),alkoxy (e.g., (CH₂)_(n)—OR, wherein n=0-10, wherein R is alkyl,(CH₂)_(n)-aryl, (CH₂)_(n)-aromatic, (CH₂)_(n)-heterocycle, substitutedor non-substituted aryl, aromatic or non-aromatic heterocycle with oneor more N, S, O, etc.), amino (e.g., alkyl amine, amino alkyl, etc.),cyano, sunlfonyl, methoxy, aldehyde, heterocycle, aromatic, combinationsthereof, etc.; and wherein L is present or absent and comprises alkylene(e.g. methylene, —CH₂—, ethylene, —CH₂—CH₂—, etc) or oxalkylene (e.g.—O—, —CH₂—O—CH₂) groups.

In some embodiments, R1 of subscaffold 1 is selected from an alkyl(e.g., branched (e.g., isopropyl), straight chain (e.g., propyl),cycloalkyl (e.g., cyclopropyl)), heteroalkyl (e.g., methyl propylether), alkyl-substituted aryl (e.g., ethylbenzene), substituted alkyl(e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g.,trifluoromethyl group), monohaloalkyl group (e.g. monofluoroethylgroup), dihaloalkyl group (e.g. difluoroethyl group), trihaloethyl group(e.g., trifluoroethyl group, See, e.g., compound 1), trihalopropyl(e.g., trifluoropropyl ((CH₂)₂CF₃), trihalobutyl group (e.g.,trifluorobutyl group ((CH₂)₃CF₃)), trihaloisopropyl (e.g.,trifluoroisopropyl (See, e.g., compound 38)), 1-fluoro,2-trifluoro,ethane (See, e.g., compound 21), 1-trifluoro, 2-ethanol (See, e.g.,compound 23)), alcohol, amino (e.g., alkyl amine, amino alkyl, etc.),cyano, sunlfonyl, methoxy, aldehyde, heterocycle, aromatic, combinationsthereof, etc.

In some embodiments, R2 of subscaffold 1 is selected from a halogen(e.g., Cl, F, Br, I), alkyl (e.g., branched, straight chain (e.g.,methyl), cycloalkyl, heteroalkyl, alkyl-substituted aryl, substitutedalkyl (e.g., halo-substituted alkyl, alcohol, amino, etc.), OH, SH, NH₂,etc.

In some embodiments, A of subscaffold 1 is selected from C, N, O, or S;wherein when A is O or S, there is no further substitution at thatrespective position; wherein, when A is N, it is optionally substitutedwith one substituent that comprises or consists of: alkyl (e.g.,branched (e.g., isopropyl), straight chain (e.g., methyl, propyl),cycloalkyl (e.g., cyclopropane, cyclopentante, cyclohexane)),heteroalkyl (e.g., methyl propyl ether (CH₂O(CH₂)₂CH₃), methylamine(CH₂NH₂), aminomethyl (CH₂NH), etc.), alkyl-substituted aryl (e.g.,methylbenzene, ethylbenzene, propylbenzene, butylbenzene, etc.),substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethylgroup (e.g., trifluoromethyl group), trihaloethyl group (e.g.,trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl),trihalobutyl group (e.g., trifluorobutyl group), trihaloisopropyl (e.g.,trifluoroisopropyl), 1-fluoro,2-trifluoro, ethane, trifluoroethanol),alcohol-substituted alkyl, amino-substituted alkyl, substitutedcycloalkyl, substituted aromatic ring (e.g., propylbenzene,1-ethyl-4methoxybenzene, 1-propyl-4-methoxy-benzene, etc.)), alcohol,amino, and/or combinations thereof; wherein when A is C, it isoptionally substituted with one or two substituents that comprises orconsists of: alkyl (e.g., branched (e.g., isopropyl), straight chain(e.g., methyl, propyl), cycloalkyl (e.g., cyclopropane, cyclopentante,cyclohexane)), heteroalkyl (e.g., methyl propyl ether, methylamino,etc.), alkyl-substituted aryl (e.g., methylbenzene, ethylbenzene,propylbenzene, butylbenzene, etc.), substituted alkyl (e.g.,halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethylgroup), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl(e.g., trifluoropropyl), trihalobutyl group (e.g., trifluorobutylgroup), trihaloisopropyl (e.g., trifluoroisopropyl),1-fluoro,2-trifluoro, ethane, trifluoroethanol), alcohol-substitutedalkyl, amino-substituted alkyl, substituted cycloalkyl, substitutedaromatic ring (e.g., propylbenzene, 1-ethyl-4methoxybenzene,1-propyl-4-methoxy-benzene, etc.)), alcohol, amino, and/or combinationsthereof.

In some embodiments, B of subscaffold 1 is selected from C, N, O, or S;wherein when B is O or S, there is no further substitution at thatrespective position; wherein, when B is N, it is optionally substitutedwith one substituent that comprises or consists of: alkyl (e.g.,branched (e.g., isopropyl), straight chain (e.g., methyl, propyl),cycloalkyl (e.g., cyclopropane, cyclopentante, cyclohexane)),heteroalkyl (e.g., methyl propyl ether, methylamino, etc.),alkyl-substituted aryl (e.g., methylbenzene, ethylbenzene,propylbenzene, butylbenzene, etc.), substituted alkyl (e.g.,halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethylgroup), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl(e.g., trifluoropropyl), trihalobutyl group (e.g., trifluorobutylgroup), trihaloisopropyl (e.g., trifluoroisopropyl),1-fluoro,2-trifluoro, ethane, trifluoroethanol), alcohol-substitutedalkyl, amino-substituted alkyl, substituted cycloalkyl, substitutedaromatic ring (e.g., propylbenzene, 1-ethyl-4-methoxybenzene,1-propyl-4-methoxy-benzene, alcohol, amino, and/or combinations thereof;wherein when B is C, it is optionally substituted with one or twosubstituents that comprises or consists of: alkyl (e.g., branched (e.g.,isopropyl), straight chain (e.g., methyl, propyl), cycloalkyl (e.g.,cyclopropane, cyclopentante, cyclohexane)), alkyl-substituted cycloalkyl(e.g. methylcyclohexyl), heteroalkyl (e.g., methyl propyl ether,methylamino, etc.), alkyl-substituted aryl (e.g., methylbenzene,ethylbenzene, propylbenzene, butylbenzene, etc.), substituted alkyl(e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g.,trifluoromethyl group), dihalomethyl group (e.g. difluoromethyl group),monohalomethyl group (3.g. monofluoromethyl group)), trihaloethyl group(e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl),trihalobutyl group (e.g., trifluorobutyl group), trihaloisopropyl (e.g.,trifluoroisopropyl), 1-fluoro, 2-trifluoro, ethane (See, e.g., compound21), trifluoroethanol), alcohol-substituted alkyl, amino-substitutedalkyl, substituted cycloalkyl, substituted aromatic ring (e.g.,propylbenzene, 1-ethyl-4methoxybenzene, 1-propyl-4-methoxy-benzene,etc.)), alcohol, amino, and/or combinations thereof (See, e.g., Table1).

In some embodiments, D of subscaffold 1 is selected from C, N, O, or S;wherein when D is O or S, there is no further substitution at thatrespective position; wherein, when D is N, it is optionally substitutedwith one substituent that comprises or consists of: alkyl (e.g.,branched (e.g., isopropyl), straight chain (e.g., methyl, propyl),cycloalkyl (e.g., cyclopropane, cyclopentante, cyclohexane)),heteroalkyl (e.g., methyl propyl ether, methylamino, etc.),alkyl-substituted aryl (e.g., methylbenzene, ethylbenzene,propylbenzene, butylbenzene, etc.), substituted alkyl (e.g.,halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethylgroup), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl(e.g., trifluoropropyl), trihalobutyl group (e.g., trifluorobutylgroup), trihaloisopropyl (e.g., trifluoroisopropyl),1-fluoro,2-trifluoro, ethane, trifluoroethanol), alcohol-substitutedalkyl, amino-substituted alkyl, substituted cycloalkyl, substitutedaromatic ring (e.g., propylbenzene, 1-ethyl-4methoxybenzene,1-propyl-4-methoxy-benzene, etc.)), alcohol, amino, and/or combinationsthereof; wherein when D is C, it is optionally substituted with one ortwo substituents that comprises or consists of: alkyl (e.g., branched(e.g., isopropyl), straight chain (e.g., methyl, propyl), cycloalkyl(e.g., cyclopropane, cyclopentante, cyclohexane)), heteroalkyl (e.g.,methyl propyl ether, methylamino, etc.), alkyl-substituted aryl (e.g.,methylbenzene, ethylbenzene, propylbenzene, butylbenzene, etc.),substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethylgroup (e.g., trifluoromethyl group), trihaloethyl group (e.g.,trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl),trihalobutyl group (e.g., trifluorobutyl group), trihaloisopropyl (e.g.,trifluoroisopropyl), 1-fluoro,2-trifluoro, ethane, trifluoroethanol),alcohol-substituted alkyl, amino-substituted alkyl, substitutedcycloalkyl, substituted aromatic ring (e.g., propylbenzene,1-ethyl-4methoxybenzene, 1-propyl-4-methoxy-benzene, etc.)), alcohol,amino, and/or combinations thereof (See, e.g., Table 1).

In some embodiments, Y of subscaffold 1 is selected from N or C.

In some embodiments, L of subscaffold 1 is alkylene (e.g. methylene,—CH₂—, ethylene, —CH₂—CH₂—, etc).

In some embodiments, compositions comprising one or more of compound1-42 of Table 1 are provided.

In some embodiments, the thienopyrimidine class compound is of a generalformula of:

wherein R1 and R2 both independently comprise or consist of: H, alkylgroup (e.g., straight-chain alkyl (e.g., methane, ethane, propane,butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane,2-methyl-hexane, 3-methyl, 2-propyl-octane, etc.), cycloalkyl (e.g.,cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane,etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane,propylcyclohexane, etc.)), a substituted alkyl group (e.g.,halogen-substituted alkyl group (e.g., mono-, di-, tetra-, penta- andtrihaloethane (e.g., trifluoroethane), halomethane (e.g.,fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane(e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol,etc.), alkylamine (e.g., primary amine (e.g., ethylamine,iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine,iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondaryamines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.),tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thiolkyl,combinations thereof, etc.), a substituted cycloalkyl group (e.g.,halogen-substituted cycloalkyl group, cycloalkoxy group,cycloalkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), aketone, a carbocyclic ring, an aromatic ring, a substituted aromaticring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene,etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), aheterocyclic aromatic ring (e.g., comprising one or more nitrogen,oxygen and/or sulfur members which may be non-substituted or substitutedwith alkyl, aryl, halogen, hydrogen bond donor or acceptor), aheterocyclic non-aromatic ring (e.g., comprising carbon and one or morenitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclicaromatic ring comprising carbon atoms and one or more nitrogen, oxygenand/or sulfur members fused to another aromatic ring, a multi-ringsystem comprising a combination of elements selected from aromaticrings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-,N-, O-, S-, and/or halogen-containing substituents, or a hydrogen bonddonor or a hydrogen bond acceptor, and/or combinations thereof; whereinR3 comprises or consists of: H, alkyl group (e.g., straight-chain alkyl(e.g., methane, ethane, propane, butane, pentane, hexane, etc.),branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane,cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl(e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), asubstituted alkyl group (e.g., halogen-substituted alkyl group (e.g.,trihaloethane (e.g., trifluoroethane), halomethane (e.g.,fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane(e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol,etc.), alkylamine (e.g., primary amine (e.g., ethylamine,iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine,iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondaryamines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.),tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl,combinations thereof, etc.), a substituted cycloalkyl group (e.g.,halogen-substituted cycloalkyl group, cycloalkoxy group,acyclolkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), aketone, a carbocyclic ring, an aromatic ring, a substituted aromaticring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene,etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), aheterocyclic aromatic ring (e.g., comprising one or more nitrogen,oxygen and/or sulfur members which may be non-substituted or substitutedwith alkyl, aryl, halogen, hydrogen bond donor or acceptor), aheterocyclic non-aromatic ring (e.g., comprising carbon and one or morenitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclicaromatic ring comprising carbon atoms and one or more nitrogen, oxygenand/or sulfur members fused to another aromatic ring, a multi-ringsystem comprising a combination of elements selected from aromaticrings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-,N-, O-, S-, and/or halogen-containing substituents, a hydrogen bonddonor or a hydrogen bond acceptor, a sulfur-containing group (e.g.,thiol, sulfide, disulfide, sulfoxide, sulfone (e.g., dimethyl sulfone,sulfonyl-amino (SO₂NH₂), sulfonyl-methane (SO₂CH₃),amino-sulfonyl-methane (NHSO₂CH₃), amino-sulfonyl-amino (NHSO₂NH₂),methyl-sulfonyl-amino (CH₂SO₂NH₂; See, e.g. compound 96),methyl-sulfonyl-methane (CH₂SO₂CH₃), methyl-sulfonyl-halomethane(CH₂SO₂CH₃)) and/or combinations thereof; wherein R³ is present at 1-4positions on the phenyl ring;wherein L is present or absent and comprises alkylene (e.g. methylene,—CH₂—, ethylene, —CH₂—CH₂—, etc) or oxalkylene (e.g. —O—, —CH₂—O—CH₂)groups;wherein Q comprises alkyl (C₁₋₅) or heteroalkyl with one or more N, Oatoms;wherein Y is N or C, and wherein when Y is C the Y position may besubstituted with R^(a), with R^(a) consisting of or comprising an alkyl(e.g., branched (e.g., isopropyl), straight chain (e.g., propyl),cycloalkyl (e.g., cyclopropyl)), heteroalkyl (e.g., methyl propylether), alkyl-substituted aryl (e.g., ethylbenzene), substituted alkyl(e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g.,trifluoromethyl group), monohaloalkyl group (e.g. monofluoroethylgroup), dihaloalkyl group (e.g. difluoroethyl group), trihaloethyl group(e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl((CH₂)₂CF₃), trihalobutyl group (e.g., trifluorobutyl group((CH₂)₃CF₃)), trihaloisopropyl (e.g., trifluoroisopropyl,1-fluoro,2-trifluoro, ethane, 1-trifluoro, 2-ethanol, alcohol (e.g.,(CH₂)_(n)OH, wherein n=0-10), alkoxy (e.g., (CH₂)_(n)—OR, whereinn=0-10, wherein R is alkyl, (CH₂)_(n)-aryl, (CH₂)_(n)-aromatic,(CH₂)_(n)-heterocycle, substituted or non-substituted aryl, aromatic ornon-aromatic heterocycle with one or more N, S, O, etc.), amino (e.g.,alkyl amine, amino alkyl, etc.), cyano, sunlfonyl, methoxy, aldehyde,heterocycle, aromatic, combinations thereof, etc.; wherein Z comprisesor consists of: H, alkyl group (e.g., straight-chain alkyl (e.g.,methane, ethane, propane, butane, pentane, hexane, etc.), branched alkylgroup (e.g., iso-propane, 2-methyl-hexane, 3-methyl, 2-propyl-octane,etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane,cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g.,methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), asubstituted alkyl group (e.g., halogen-substituted alkyl group (e.g.,trihaloethane (e.g., trifluoroethane), halomethane (e.g.,fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane(e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol,etc.), alkylamine (e.g., primary amine (e.g., ethylamine,iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine,iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondaryamines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.),tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl,a substituted cycloalkyl group (e.g., halogen-substituted cycloalkylgroup, cycloalkoxy group, acyclolkylamine, etc.), a halogen (e.g., F,Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, asubstituted aromatic ring (e.g., branched aromatic ring (e.g.,ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene,fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprisingone or more nitrogen, oxygen and/or sulfur members which may benon-substituted or substituted with alkyl, aryl, halogen, hydrogen bonddonor or acceptor), a heterocyclic non-aromatic ring (e.g., comprisingcarbon and one or more nitrogen, oxygen and/or sulfur members),carbocyclic or heterocyclic aromatic ring comprising carbon atoms andone or more nitrogen, oxygen and/or sulfur members fused to anotheraromatic ring, a multi-ring system comprising a combination of elementsselected from aromatic rings, cycloalkane, heterocyclic rings, alkylchains, and suitable C-, N-, O-, S-, and/or halogen-containingsubstituents, a hydrogen bond donor or a hydrogen bond acceptor, asulfur-containing group (e.g., thiol, sulfide, disulfide, sulfoxide,sulfone), a group selected from CHR⁴SO₂R⁵ or NR⁴SO₂R⁵, in which R⁴comprises or consists of: H, alkyl group (e.g., straight-chain alkyl(e.g., methane, ethane, propane, butane, pentane, hexane, etc.),branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane,cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl(e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), asubstituted alkyl group (e.g., halogen-substituted alkyl group (e.g.,trihaloethane (e.g., trifluoroethane), alkylnitrile group (e.g.ethanenitryle group, CH₂CN), alkoxy group (e.g., ether, alcohol, etc.),alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine,n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine,methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g.,dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine(e.g., trimethylamine, triphenylamine, etc.), a carbocyclic ring, asubstituted cycloalkyl group (e.g., halogen-substituted cycloalkylgroup, alkyl-substituted cycloalkyl group, cycloalkoxy group,cyclolkylamine, etc.) and R⁵ comprises or consists of: H, alkyl group(e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane,pentane, hexane, etc.), branched alkyl group (e.g., iso-propane,2-methyl-hexane, 3-methyl, 2-propyl-octane, etc.), cycloalkyl (e.g.,cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane,etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane,propylcyclohexane, etc.)), a substituted alkyl group (e.g.,halogen-substituted alkyl group (e.g., trihaloethane (e.g.,trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane(e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.),alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primaryamine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine,iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine,etc.), secondary amines (e.g., dimethylamine, methylethanolamine,diphenylamine, etc.), tertiary amine (e.g., trimethylamine,triphenylamine, etc.), thioalkyl, a substituted cycloalkyl group (e.g.,halogen-substituted cycloalkyl group, cycloalkoxy group,acyclolkylamine, etc.), a ketone, a carbocyclic ring, an aromatic ring,a substituted aromatic ring (e.g., branched aromatic ring (e.g.,ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene,fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprisingone or more nitrogen, oxygen and/or sulfur members which may benon-substituted or substituted with alkyl, aryl, halogen, hydrogen bonddonor or acceptor), a heterocyclic non-aromatic ring (e.g., comprisingcarbon and one or more nitrogen, oxygen and/or sulfur members),carbocyclic or heterocyclic aromatic ring comprising carbon atoms andone or more nitrogen, oxygen and/or sulfur members fused to anotheraromatic ring, a multi-ring system comprising a combination of elementsselected from aromatic rings, cycloalkane, heterocyclic rings, alkylchains, and suitable C-, N-, O-, S-, and/or halogen-containingsubstituents, a hydrogen bond donor or a hydrogen bond acceptor, and/orcombinations thereof, R⁵ might also be a part of the 3-8 member aromaticor non-aromatic ring comparising C, N, O, S (e.g. compounds 52, 53, 55).In some embodiments, Z comprises:

In some embodiments, Z is selected from: dimethyl sulfone,amino-sulfonyl-methane (NHSO₂CH₃), amino-sulfonyl-amine (NHSO₂NH₂),methyl-sulfonyl-amino (CH₃SO₂NH₂, methylamino-sulfonyl-methane(NCH₃SO₂CH₃; See e.g., compound 46), amino-sulfonyl-amino-methane(NHSO₂NHCH3), amino-sulfonyl-ethane-2-amine (NHSO₂CH₂CH₂NH₂),amino-sulfonyl-ethane (NHSO₂CH₂CH₃), amino-sulfonyl-dimethylamine(NHSO₂N(CH3)₂; See, e.g., compound 51), amino-sulfonyl-isopropane (NHSO₂^(i)Pr), amino-sulfonyl-heterocycloalkane (e.g.,amino-sulfonyl-1-pyridine, amino-sulfonyl-1-oxazine,amino-sulfonyl-1-pyrazine, etc.), amino-sulfonyl-alkyl (e.g.,amino-sulfonyl-methane (NHSO₂CH₃), amino-sulfonyl-ethane (NHSO₂CH₂CH₃),amino-sulfonyl-propane (NHSO₂(CH₂)₂CH₃), amino-sulfonyl-butane(NHSO2(CH₂)₃CH₃), etc.), sulfinic acid, thiocyante, etc.), and/orcombinations thereof.

In some embodiments, R1 of subscaffold 2 is selected from an alkyl(e.g., branched (e.g., isopropyl), straight chain (e.g., propyl),cycloalkyl (e.g., cyclopropyl)), heteroalkyl (e.g., methyl propylether), alkyl-substituted aryl (e.g., ethylbenzene), substituted alkyl(e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g.,trifluoromethyl group), trihaloethyl group (e.g., trifluoroethyl group),trihalopropyl (e.g., trifluoropropyl), trihalobutyl group (e.g.,trifluorobutyl group), trihaloisopropyl (e.g., trifluoroisopropyl),1-fluoro,2-trifluoro, ethane, trifluoroethanol), alcohol, amino, etc.(See, e.g., Table 2).

In some embodiments, R2 of subscaffold 2 is selected from a halogen(e.g., Cl, F, Br, I), alkyl (e.g., branched, straight chain (e.g.,methyl), cycloalkyl, heteroalkyl, etc.), alkyl-substituted aryl,substituted alkyl (e.g., halo-substituted alkyl, alcohol, amino, etc.),alcohol (e.g. OH, methanol, ethanol, etc), SH, NH₂, etc.

In some embodiments, R3 of subscaffold 2 is selected from hydrogen,alkyl (C₁-C₅), haloalkyl (e.g. CF₃), alcohol (e.g., OH, methanol,ethanol, isopropanol, etc.), alkoxy (e.g. methoxy, ethoxy, etc), amine(e.g. —NH2), halogen (Cl, Br, F, I), methyl-sulfonyl-amine (CH₂SO₂NH₂),etc. (See, e.g., Table 2). In some embodiments, R³ can be present atmore than 1 position of the phenyl ring.

In some embodiments, R3 of subscaffold 2 is present at the ortho or metapositions of the benzene ring. In some embodiments, R3 groups arepresent at two or more positions on the benzene.

In some embodiments, Z of subscaffold 2 comprises an H, alkyl group,amino group (e.g., primary, secondary, alkylamine, aminoalkyl, etc.),halogen, heterocycle, sulfone-containing group (see e.g., Table 2),CHR⁴SO₂R⁵ or NR⁴SO₂R⁵ in which R4 and R5 are independently selected froman alkyl (e.g., branched, straight chain (e.g., methyl), cycloalkyl,heteroalkyl, etc.), substituted or non-substituted heterocyclecomprising one or more N, C, O or S, thrihaloalkane, amino, alcohol,alkyl-substituted aryl, substituted or non-substituted heterocyclicring, substituted alkyl (e.g., halo-substituted alkyl, alcohol, amino,cyano, aryl, heterocyclic ring, etc.), cyano, etc.

In some embodiments, R3 and Z groups (e.g., (CH)₂NH in compound 81)bridge two positions of the benzene ring of subscaffold 2.

In some embodiments, L of subscaffold 2 is alkylene (e.g. ethylene,—CH₂—CH₂—, etc).

In some embodiments, Q of subscaffold 2 is alkylene (e.g. C1-C5) oroxyalkylene (e.g. —CH₂—O—CH₂—).

In some embodiments, compositions comprising one or more of compound43-104 of Table 2 are provided.

In some embodiments, the thienopyrimidine class compound is of a generalformula of:

wherein R1, R2, R3, and R4 independently comprise or consist of: H,alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane,butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane,2-methyl-hexane, 3-methyl, 2-propyl-octane, etc.), cycloalkyl (e.g.,cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane,etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane,propylcyclohexane, etc.)), a substituted alkyl group (e.g.,halogen-substituted alkyl group (e.g., mono-, di-, tetra-, penta- andtrihaloethane (e.g., trifluoroethane), halomethane (e.g.,fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane(e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol,etc.), alkylamine (e.g., primary amine (e.g., ethylamine,iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine,iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondaryamines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.),tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thiolkyl,combinations thereof, etc.), a substituted cycloalkyl group (e.g.,halogen-substituted cycloalkyl group, cycloalkoxy group,acyclolkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), aketone, a carbocyclic ring, an aromatic ring, a substituted aromaticring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene,etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), aheterocyclic aromatic ring (e.g., comprising one or more nitrogen,oxygen and/or sulfur members which may be non-substituted or substitutedwith alkyl, aryl, halogen, hydrogen bond donor or acceptor), aheterocyclic non-aromatic ring (e.g., comprising carbon and one or morenitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclicaromatic ring comprising carbon atoms and one or more nitrogen, oxygenand/or sulfur members fused to another aromatic ring, a multi-ringsystem comprising a combination of elements selected from aromaticrings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-,N-, O-, S-, and/or halogen-containing substituents, or a hydrogen bonddonor or a hydrogen bond acceptor, and/or combinations thereof; whereinR5 comprises or consists of: H, alkyl group (e.g., straight-chain alkyl(e.g., methane, ethane, propane, butane, pentane, hexane, etc.),branched alkyl group (e.g., iso-propanol, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane,cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl(e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), asubstituted alkyl group (e.g., halogen-substituted alkyl group (e.g.,trihaloethane (e.g., trifluoroethane), halomethane (e.g.,fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane(e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol,etc.), alkylamine (e.g., primary amine (e.g., ethylamine,iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine,iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondaryamines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.),tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thiolkyl,combinations thereof, etc.), amide, alkylamide, a substituted cycloalkylgroup (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group,acyclolkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), aketone, a carbocyclic ring, an aromatic ring, a substituted aromaticring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene,etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), aheterocyclic aromatic ring (e.g., comprising one or more nitrogen,oxygen and/or sulfur members which may be non-substituted or substitutedwith alkyl, aryl, halogen, hydrogen bond donor or acceptor), aheterocyclic non-aromatic ring (e.g., comprising carbon and one or morenitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclicaromatic ring comprising carbon atoms and one or more nitrogen, oxygenand/or sulfur members fused to another aromatic ring, a multi-ringsystem comprising a combination of elements selected from aromaticrings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-,N-, O-, S-, and/or halogen-containing substituents, or a hydrogen bonddonor or a hydrogen bond acceptor, and/or combinations thereof. In someembodiments, R5 is present at the ortho, meta, or para position of thebenzene ring of subscaffold 3. In some embodiments, the benzene ring ofsubscaffold 3 comprises R5 groups at two or more (e.g., 2, 3, 4, or 5)positions. In some embodiments, an R5 group bridges two positions of thebenzene ring of subscaffold 3 (See e.g., 3-keto,4-amino-propane ofcompound 136 of Table 3); and wherein Y is N or C, and wherein when Y isC the Y position may be substituted with R^(a), with R^(a) consisting ofor comprising an alkyl (e.g., branched (e.g., isopropyl), straight chain(e.g., propyl), cycloalkyl (e.g., cyclopropyl)), heteroalkyl (e.g.,methyl propyl ether), alkyl-substituted aryl (e.g., ethylbenzene),substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethylgroup (e.g., trifluoromethyl group), monohaloalkyl group (e.g.monofluoroethyl group), dihaloalkyl group (e.g. difluoroethyl group),trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g.,trifluoropropyl ((CH₂)₂CF₃), trihalobutyl group (e.g., trifluorobutylgroup ((CH₂)₃CF₃)), trihaloisopropyl (e.g., trifluoroisopropyl,1-fluoro,2-trifluoro, ethane, 1-trifluoro,2-ethanol, alcohol (e.g.,(CH₂)_(n)OH, wherein n=0-10), alkoxy (e.g., (CH₂)_(n)—OR, whereinn=0-10, wherein R is alkyl, (CH₂)_(n)-aryl, (CH₂)_(n)-aromatic,(CH₂)_(n)-heterocycle, substituted or non-substituted aryl, aromatic ornon-aromatic heterocycle with one or more N, S, O, etc.), amino (e.g.,alkyl amine, amino alkyl, etc.), cyano, sunlfonyl, methoxy, aldehyde,heterocycle, aromatic, combinations thereof, etc.; and wherein L ispresent or absent and comprises alkylene (e.g. methylene, —CH₂—,ethylene, —CH₂—CH₂—, propylene, —CH₂—CH₂—CH₂—, etc) or oxalkylene (e.g.—O—, —CH₂—O—CH₂) groups.

In some embodiments, R1 of subscaffold 3 comprises or consists oftrifluoroethane. In some embodiments, R1 of subscaffold 3 comprises orconsists of trihaloethane (e.g., trifluoroethane), 2-dihalo-4-butanol(e.g., 2-difluoro-4-butanol, etc.), an alkyl chain (e.g., straight chainalkyl (e.g., methane, ethane, propane, butane, etc.), branched alkyl,cycloalkyl, or combinations thereof), 2-dihalo-propane (e.g.,2-difluoro-propane, etc.), etc. (See Table 3).

In some embodiments, R2 of subscaffold 3 is selected from a halogen(e.g., Cl, F, Br, I), alkyl (e.g., branched, straight chain (e.g.,methyl), cycloalkyl, heteroalkyl, etc.), alkyl-substituted aryl,substituted alkyl (e.g., halo-substituted alkyl, alcohol, amino, etc.),alcohol (—OH, —CH₂OH, etc) SH, NH₂, etc.

In some embodiments, R3 of subscaffold 3 consists of H. In someembodiments, R3 of subscaffold 3 comprises or consists of an alkyl(e.g., methane, ethane, propane, butane, etc.), amine (e.g., NH₂,NH-alkyl (e.g., NH-methyl, NH-ethyl, NH—CH₂-Ph, etc.), NH-alcohol (e.g.,NH—CH₂—CH₂—OH), etc.), alcohol (e.g., methanol, ethanol, butanol,propanol, —CH₂—CHOHCH₂OH, etc.), halo-substituted alkyl, combinationsthereof, etc. (See Table 3). In some embodiments, R3 is fused in a ringwith R2 (See, e.g. compound 158).

In some embodiments, R4 of subscaffold 4 comprises or consists of anamine (e.g., NH₂, alkylamine (e.g., methylamine, ethylamine,propylamine, etc.), aminoalkyl (e.g., straight chain alkyl, cycloalkyl,or combinations thereof (See, e.g., compound 171)), amino-alkyl-phenyl(e.g., amino-methyl-phenyl, amino-ethyl-phenyl, etc.), etc.), alcohol(e.g., OH, methanol, ethanol, propanol, isopropanol, etc.), substitutedamine (—NHR³) or substituted alcohol (—OR³), in which R³ is alkyl,alkyl-aryl (substituted and non-substituted), alkyl-cycloalkyl(substituted and non-substituted), alkyl-aromatic ring substituted ornon-substituted, alkyl-non aromatic ring (C,N,O,S) substituted ornon-substituted, or any of the R4 groups depicted in Tables 4, 5, or 7.In some embodiments, R4 comprises or consists of aminomethyl phenyl(See, e.g. compound 167), aminoethyl phenyl (See, e.g., compound 168),amino-methyl-cyclopentane (See, e.g., compound 169), aminomethyl,n-methanal pyrrolidine, aminoethyl cyclopentane, aminomethyl (NHCH₃),methylamine (CH₂NH₂), n-sulfonyl-methylpyrrolidine (See, e.g., compound173), O-methyl phenyl (See, e.g. compound 174), etc., see Table 4.

In some embodiments, R5 of subscaffold 3 comprises or consists of: H, analcohol (e.g., OH, methanol, ethanol, etc.), alkane, cycloalkane (e.g.,substituted cycloalkane (e.g., cyanocyclopropane)), amine, halogen(e.g., chlorine, fluorine, bromine, iodine, etc.), heterocyclic ring(e.g., attached at any position on the heterocyclic ring: morpholine,piperidine, methylpiperidine, pyrrole, thiophene, piperazine, etc.),alkylamine (e.g., methylamine, ethylamine, propylamine,1,4-dimethyl-piperazine, etc.), alkylalkohol (e.g. —CH₂OH), alkoxy,carboxamido, O-dihalomethane, sulfonyl-amine, trihalomethane (e.g.,trifluoromethane), etc. In some embodiments, the benzene ring ofsubscaffold 3 comprises R5 groups at two or more (e.g., 2, 3, 4, or 5)positions.

In some embodiments, L of subscaffold 3 is alkylene (e.g. ethylene,—CH₂—CH₂—, compound 135).

In some embodiments, compositions comprising one or more of compound105-159 of Table 3, 165-174 of Table 4 and 280 and 282 of Table 7 areprovided.

In some embodiments, the thienopyrimidine class compound is of a generalformula of:

wherein R1, R2, R3, R4, R5, R6, R7, R8 each independently comprise orconsist of: H, alkyl group (e.g., straight-chain alkyl (e.g., methane,ethane, propane, butane, pentane, hexane, etc.), branched alkyl group(e.g., iso-propanel, 2-methyl-hexane, 3-methyl, 2-propyl-octane, etc.),cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane,cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane,ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group(e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g.,trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane(e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.),alkoxy group (e.g., ether, alcohol, etc.), amine, alkylamine (e.g.,primary amine (e.g., ethylamine, iso-butylamine, n-propylamine,sec-butylamine, iso-propylamine, iso-amylamine, methylamine,dimethylamine, n-amylamine, etc.), secondary amines (e.g.,dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine(e.g., trimethylamine, triphenylamine, etc.), thiolkyl, combinationsthereof, etc.), a substituted cycloalkyl group (e.g.,halogen-substituted cycloalkyl group, cycloalkoxy group,acyclolkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), aketone, an amide, an alkylamide, a cyano group, methyl carbonitrile(e.g. CH₂CN), —SO₂CH₃ group, sulfonyl group, a carbocyclic ring, anaromatic ring, a substituted aromatic ring (e.g., branched aromatic ring(e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g.,chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring(e.g., comprising one or more nitrogen, oxygen and/or sulfur memberswhich may be non-substituted or substituted with alkyl, aryl, halogen,hydrogen bond donor or acceptor), a substituted or non-substitutedheterocyclic non-aromatic ring (e.g., comprising carbon and one or morenitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclicaromatic ring comprising carbon atoms and one or more nitrogen, oxygenand/or sulfur members fused to another aromatic ring, a multi-ringsystem comprising a combination of elements selected from aromaticrings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-,N-, O-, S-, and/or halogen-containing substituents, or a hydrogen bonddonor or a hydrogen bond acceptor, and/or combinations thereof; and

wherein any of the H atoms, R6, R7 and R8 on the indole of subscaffold 4may be replaced with one of: halogen (e.g., F, Cl, Br, I, etc.), alcohol(e.g., OH, methanol, ethanol, etc.), alkyl (C1-C5), alkoxy (e.g.methoxy, ethoxy, etc), amine (e.g. NH₂, methylamine, ethylamine, etc),cyano group (e.g., CN, methyl carbonitrile, ethyl carbonitrile, etc.),an amide (e.g. CONH₂, acetamide, etc), —SO₂CH₃ group; wherein R6 can bepresent on either the benzyl and/or pyrole portion of the indole ring,and wherein R6 can be present at one or more of the positions of thebenzyl and/or pyrole portion of the indole ring that are not otherwiseoccupied by a substituent; and wherein Y is N or C, and wherein when Yis C the Y position may be substituted with R^(a), with R^(a) consistingof or comprising an alkyl (e.g., branched (e.g., isopropyl), straightchain (e.g., propyl), cycloalkyl (e.g., cyclopropyl)), heteroalkyl(e.g., methyl propyl ether), alkyl-substituted aryl (e.g.,ethylbenzene), substituted alkyl (e.g., halo-substituted alkyl (e.g.,trihalomethyl group (e.g., trifluoromethyl group), monohaloalkyl group(e.g. monofluoroethyl group), dihaloalkyl group (e.g. difluoroethylgroup), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl(e.g., trifluoropropyl ((CH₂)₂CF₃), trihalobutyl group (e.g.,trifluorobutyl group ((CH₂)₃CF₃)), trihaloisopropyl (e.g.,trifluoroisopropyl, 1-fluoro,2-trifluoro, ethane, 1-trifluoro,2-ethanol), alcohol (e.g., (CH₂)_(n)OH, wherein n=0-10), alkoxy (e.g.,(CH₂)_(n)—OR, wherein n=0-10, wherein R is alkyl, (CH₂)_(n)-aryl,(CH₂)_(n)-aromatic, (CH₂)_(n)-heterocycle, substituted ornon-substituted aryl, aromatic or non-aromatic heterocycle with one ormore N, S, O, etc.), amino (e.g., alkyl amine, amino alkyl, etc.),cyano, sunlfonyl, methoxy, aldehyde, heterocycle, aromatic, combinationsthereof, etc.;

wherein L is present or absent, and if present it comprises alkylene(e.g. methylene, —CH₂—, ethylene, —CH₂—CH₂—, propylene, —CH₂—CH₂—CH₂—,etc) or oxalkylene (e.g. —O—, —CH₂—O—CH₂) groups.

In some embodiments, R1 of subscaffold 4 comprises or consists oftrihaloethane (e.g., trifluoroethane) group, (see Table 5).

In some embodiments R2 is H or another R2 substituent described herein.

In some embodiments R3 of subscaffold 4 comprises or consists of analkyl (e.g., methane, ethane, propane, butane, etc.), amine (e.g., NH₂,NH-alkyl (e.g., NH-methyl, NH-ethyl, NH—CH₂-Ph, etc.), NH-alcohol (e.g.,NH—CH₂—CH₂—OH), etc.), an alcohol (e.g., methanol, ethanol, butanol,propanol, CH₂CHOHCH₂OH, etc.), a heterocyclic ring, analkyl-heterocyclic ring (e.g., ethyl-morpholine (see compound 238),propyl-indole, etc.), etc. In some embodiments, R3 is fused in a ringwith R2 (See, e.g. compound 158).

In some embodiments R4 comprises or consists of amine (e.g. —NH₂),aminomethyl, n-methanal pyrrolidine (see compound 161 in Table 5),—CH₂—OH (see compounds 163-164 in Table 5).

In some embodiments, R5 is —CH₂—OH (see compound 211, Table 5).

In some embodiments, R6 is an alkyl (e.g., methane, ethane, propane,butane, etc.), halogen (e.g., Br, F, Cl, I, etc.), haloalkane, amine(e.g., NH₂, NH-alkyl (e.g., NH-methyl, NH-ethyl, NH—CH₂-Ph, etc.),O-alkyl (e.g., OCH₃, OCH₂CH₃, etc.), NH-alcohol (e.g., NH—CH₂—CH₂—OH),etc.), an alcohol (e.g., methanol, ethanol, butanol, propanol,CH₂CHOHCH₂OH, etc.), or any R6 group of Tables 4, 5, or 7. In someembodiments, R6 is present on either the benzyl and/or pyrrole portionsof the indole ring. In some embodiments R6 on indole ring is present atmore than one position on the benzyl and/or pyrrole portions of theindole ring.

In some embodiments, R7 is H, alkyl (e.g., methyl, ethyl, propyl, butyl,etc.), haloalkane, cycloalkyl (e.g., cyclopropane (e.g., methylcyclopropane), cyclobutane, cyclopentane, cyclohexane, etc.), an alcohol(e.g., OH, methanol, ethanol, propanol, butanol, etc.), a substituted ornon-substituted heteroaromatic ring (e.g., pyrazole, triazole (e.g.,1,2,4 triazole), isoxazole (e.g., dimethyl isoxazole), (CH₂)_(n)—OR(wherein n=1-10 and R is an aromatic ring, heteroaromatic ring,cycloalkyl, heterocycle, substituted ring, etc.), (CH₂)_(n)—R (whereinn=1-10 and R is an aromatic ring, heteroaromatic ring, cycloalkyl,heterocycle, substituted ring, etc.), (CH₂)_(n)—O—(CH₂)_(m)—R (whereinn=1-10, m=1-10, and R is an aromatic ring, heteroaromatic ring,cycloalkyl, heterocycle, substituted ring, etc.), alkyl-heteroaromaticring (e.g. CH₂-pyrazole, CH₂-triazole, CH₂—CH₂-triazole, etc), amide(e.g. acetamide, see, e,g, compound 189), amine (e.g., NH₂, NH-alkyl(e.g., NH-methyl, NH-ethyl, NH—CH₂-Ph, etc., NH-alcohol (e.g.,NH—CH₂—CH₂—OH), etc.), substituted or non-substituted alcohol (e.g.,methanol, ethanol, butanol, propanol, CH₂CHOHCH₂OH, etc.), or any R7substituents in the compounds of Tables 4, 5, or 7.

In some embodiments, R8 of subscaffold 4 comprises or consists of: H,alkyl (e.g., methyl, ethyl, propyl, butyl, etc.), cycloalkyl (e.g.,cyclopropane (e.g., methyl cyclopropane), cyclobutane, cyclopentane,cyclohexane, etc.), a primary alcohol (e.g., OH, methanol, ethanol,propanol, butanol, etc.), a secondary alcohol, a substituted ornon-substituted heteroaromatic ring (e.g., pyrazole, triazole (e.g.,1,2,4 triazole), isoxazole, isopropylisopropanolamine(CH₂CHOHCH₂NHCH(CH₃)₂); sulfonamide, a cyano group (e.g., CN, methylcarbonitrile, ethyl carbonitrile, propyl carbonitrile, etc.), amide(e.g., CONH₂, methylcarboxamido (e.g., CH₂CONH₂), ethyl carboxamido(CH₂CH₂CONH₂), carboxyamido-methane (e.g., CONHCH₃ or NHCOCH₃), etc.),methylsulfonyl, sulfonamide, ketone (e.g., ═O), or any R8 substituentsin the compounds of Tables 4, 5, or 7.

In some embodiments, the substituted indole ring of subscaffold 4 is:cyano substituted (e.g., 1-carbonitrile, 2-carbonitrile, etc.),methyl-carbonitrile substituted (e.g., 5-methyl-carbonitrile, etc.),methylcyclopropane substituted (e.g., 1-methylcyclopropane),halo-substituted (e.g., 3-halo (e.g., 3-fluoro, 4-fluoro, 6-fluoro,etc.)), alkyl substituted (e.g., 1-alkyl (e.g., 1-methyl, 1-ethyl,1-propyl, etc.)), alcohol-substituted (e.g., OH substituted (e.g.,6-OH), methanol substituted (e.g., 1-methanol), ethanol substituted(e.g., 1-ethanol), etc.), O-methyl substituted (e.g., 4-O-methyl,6-O-methyl, etc.), alkoxy substituted (e.g. 1-O-methoxy, 1-O-ethoxy,etc), heterocyclic aromatic ring (or ring system) substituted (e.g.,imidazole), amine substituted (e.g., NH₂, methylamine, ethylamine (e.g.,1-ethylamine, etc.), aminomethyl, etc.), dihydroxy substituted (e.g.,1,2-propanediol, etc.), amide substituted (e.g., 1-propanamide),acetamide, 1-methyl 1,2,3-triazole substituted, 1-ethyl imidazolesubstituted, heterocycle substituted, carboxamido substituted (e.g.,1-carboxamido), sulfonyl substituted (e.g., 1-sulfonyl methyl (SO₂CH₃),ether substituted (e.g., isopropanol methyl ether (CH₂CHOHCH₂CH₃),keto-substituted (e.g., 1-keto), isopropanol-amine-isopropyl substituted(CH₂CHOHCH₂NHCH(CH₃)₂, combinations thereof depicted in Table 4, orcombinations thereof not depicted in Table 4).

In some embodiments, L is H.

In some embodiments, compositions comprising one or more of compound160-164 (Table 4) and 175-252 of Table 5 and compounds 278, 279, 281 ofTable 7 are provided.

In some embodiments, the thienopyrimidine class compound is of a generalformula of:

wherein R1, R², R³ and R⁴ independently comprise or consist of: H,alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane,butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane,2-methyl-hexane, 3-methyl, 2-propyl-octane, etc.), cycloalkyl (e.g.,cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane,etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane,propylcyclohexane, etc.)), a substituted alkyl group (e.g.,halogen-substituted alkyl group (e.g., trihaloethane (e.g.,trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane(e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.),alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primaryamine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine,iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine,etc.), secondary amines (e.g., dimethylamine, methylethanolamine,diphenylamine, etc.), tertiary amine (e.g., trimethylamine,triphenylamine, etc.), thiolkyl, combinations thereof, etc.), asubstituted cycloalkyl group (e.g., halogen-substituted cycloalkylgroup, cycloalkoxy group, acyclolkylamine, etc.), a halogen (e.g., F,Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, asubstituted aromatic ring (e.g., branched aromatic ring (e.g.,ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene,fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprisingone or more nitrogen, oxygen and/or sulfur members which may benon-substituted or substituted with alkyl, aryl, halogen, hydrogen bonddonor or acceptor), a heterocyclic non-aromatic ring (e.g., comprisingcarbon and one or more nitrogen, oxygen and/or sulfur members),carbocyclic or heterocyclic aromatic ring comprising carbon atoms andone or more nitrogen, oxygen and/or sulfur members fused to anotheraromatic ring, a multi-ring system comprising a combination of elementsselected from aromatic rings, cycloalkane, heterocyclic rings, alkylchains, and suitable C-, N-, O-, S-, and/or halogen-containingsubstituents, or a hydrogen bond donor or a hydrogen bond acceptor,and/or combinations thereof; and

wherein any of the H atoms on the benzene ring of subscaffold 5 may bereplaced with one of: halogen (e.g., F, Cl, Br, I, etc.), alcohol (e.g.,OH, methanol, ethanol, etc.), cyano group (e.g., CN, methylcarbonitrile, ethyl carbonitrile, etc.), amine (e.g. NH₂, methylamine,ethylamine, etc.), trifluoromethane, alkyl (e.g., methane, ethane,propane, etc.), alkoxy (e.g. methoxy, ethoxy, etc), halogen substitutedalkoxy (e.g. trifluoromethoxy), ketone, sulfonyl group (e.g.slufonamide), substituted or non-substituted heterocyclic ring (e.g.comprising carbon and one or more nitrogen oxygen and/or sulfurmembers), etc.; and wherein Y is N or C, and wherein when Y is C the Yposition may be substituted with R^(a), with R^(a) consisting of orcomprising an alkyl (e.g., branched (e.g., isopropyl), straight chain(e.g., propyl), cycloalkyl (e.g., cyclopropyl)), heteroalkyl (e.g.,methyl propyl ether), alkyl-substituted aryl (e.g., ethylbenzene),substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethylgroup (e.g., trifluoromethyl group), monohaloalkyl group (e.g.monofluoroethyl group), dihaloalkyl group (e.g. difluoroethyl group),trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g.,trifluoropropyl ((CH₂)₂CF₃), trihalobutyl group (e.g., trifluorobutylgroup ((CH₂)₃CF₃)), trihaloisopropyl (e.g., trifluoroisopropyl,1-fluoro, 2-trifluoro, ethane, 1-trifluoro, 2-ethanol), alcohol (e.g.,(CH₂)_(n)OH, wherein n=0-10), alkoxy (e.g., (CH₂)_(n)—OR, whereinn=0-10, wherein R is alkyl, (CH₂)_(n)-aryl, (CH₂)_(n)-aromatic,(CH₂)_(n)-heterocycle, substituted or non-substituted aryl, aromatic ornon-aromatic heterocycle with one or more N, S, O, etc.), amino (e.g.,alkyl amine, amino alkyl, etc.), cyano, sunlfonyl, methoxy, aldehyde,heterocycle, aromatic, combinations thereof, etc.;

In some embodiments, R1 of subscaffold 5 comprises or consists of: H,trifluoroethane, or another R1 group provided herein.

In some embodiments, R2 of subscaffold 5 comprises or consists of H.

In some embodiments, R3 of subscaffold 5 comprises or consists of alkylgroup (e.g. n-buthyl, compound 264).

In some embodiments, R⁴ of subscaffold 5 comprises or consists of: H,aminosulfonyl, halogen (e.g., Cl, Br, F, I, etc.), a substituted ornon-substituted heterocycle (e.g., piperidine, 1,4-oxazinane,piperazine, morpholine), cyano group (e.g., CN, cyanomethane,cyanoethane, etc.), alkoxy (e.g. O-methyl), amine (e.g. NH₂,methylamine, ethylamine, etc.), alcohol (e.g., OH, methanol, ethanol,etc.), trifluoromethane, ketone (e.g. acetyl), halogen substitutedalkoxy (e.g. O-trifluoromethane, OCF₃, alkyl (e.g., methane, ethane,propane, etc.), etc.

In some embodiments, compositions comprising one or more of compound253-277 of Table 6 are provided.

In some embodiments, the thienopyrimidine class compound is of a generalformula of:

wherein Q, R1 and R2 comprises or consists of: H, an alkyl group (e.g.,straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane,hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane,3-methyl, 2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane,cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branchedcyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane,propylcyclohexane, etc.)), a substituted alkyl group (e.g.,halogen-substituted alkyl group (e.g., trihaloethane (e.g.,trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane(e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.),alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primaryamine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine,iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine,etc.), secondary amines (e.g., dimethylamine, methylethanolamine,diphenylamine, etc.), tertiary amine (e.g., trimethylamine,triphenylamine, etc.), thiolkyl, combinations thereof, etc.), asubstituted cycloalkyl group (e.g., halogen-substituted cycloalkylgroup, cycloalkoxy group, acyclolkylamine, etc.), a halogen (e.g., F,Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, asubstituted aromatic ring (e.g., branched aromatic ring (e.g.,ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene,fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprisingone or more nitrogen, oxygen and/or sulfur members which may benon-substituted or substituted with alkyl, aryl, halogen, hydrogen bonddonor or acceptor), a heterocyclic non-aromatic ring (e.g., comprisingcarbon and one or more nitrogen, oxygen and/or sulfur members),carbocyclic or heterocyclic aromatic ring comprising carbon atoms andone or more nitrogen, oxygen and/or sulfur members fused to anotheraromatic ring, a multi-ring system comprising a combination of elementsselected from aromatic rings, cycloalkane, heterocyclic rings, alkylchains, and suitable C-, N-, O-, S-, and/or halogen-containingsubstituents, or a hydrogen bond donor or a hydrogen bond acceptor,and/or combinations thereof; and wherein Y is N or C, and wherein when Yis C the Y position may be substituted with R^(a), with R^(a) consistingof or comprising an H, alkyl (e.g., branched (e.g., isopropyl), straightchain (e.g., propyl), cycloalkyl (e.g., cyclopropyl)), heteroalkyl(e.g., methyl propyl ether), alkyl-substituted aryl (e.g.,ethylbenzene), substituted alkyl (e.g., halo-substituted alkyl (e.g.,trihalomethyl group (e.g., trifluoromethyl group), monohaloalkyl group(e.g. monofluoroethyl group), dihaloalkyl group (e.g. difluoroethylgroup), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl(e.g., trifluoropropyl ((CH₂)₂CF₃), trihalobutyl group (e.g.,trifluorobutyl group ((CH₂)₃CF₃)), trihaloisopropyl (e.g.,trifluoroisopropyl), 1-fluoro, 2-trifluoro, ethane, 1-trifluoro,2-ethanol), alcohol (e.g., (CH₂)_(n)OH, wherein n=0-10), alkoxy (e.g.,(CH₂)_(n)—OR, wherein n=0-10, wherein R is alkyl, (CH₂)_(n)-aryl,(CH₂)_(n)-aromatic, (CH₂)_(n)-heterocycle, substituted ornon-substituted aryl, aromatic or non-aromatic heterocycle with one ormore N, S, O, etc.), amino (e.g., alkyl amine, amino alkyl, etc.),cyano, sunlfonyl, methoxy, aldehyde, heterocycle, aromatic, combinationsthereof, etc.; and wherein L is present or absent and comprises alkylene(e.g. methylene, —CH₂—, ethylene, —CH₂—CH₂—, etc) or oxalkylene (e.g.—O—, —CH₂—O—CH₂) groups.

In some embodiments, the present invention provides a compositioncomprising a compound having the structure of one or subscaffolds 1-6;wherein any of R1-R5, A, B, D, Q, L, W, X, Y, and Z each independentlycomprise organic substituents comprising fewer than 40 atoms selectedfrom C, H, N, O, P, S, Cl, Br, F, and I. In some embodiments, thecompound is selected from compounds 1-283. In some embodiments, R1 isCH₂CF₃.

In some embodiments, a compound of the present invention has a generalstructure of one of:

In some embodiments, all substituents (e.g., R1-R8, A, B, D, L, Q, X, Y,and Z) independently consist of or comprise any of the functional groupsset forth herein, and in any suitable combination.

In some embodiments, R1-R8, when present on a subscaffold, eachindependently comprise or consist of any suitable combination of: C₁-C₁₀alkanes (e.g., straight, branched, or cyclic), halogens (e.g., Cl, Br,F, or I), OH groups (e.g., alkyl-OH), O-alkyl groups, NH₂ groups,N-dialkyl, NH-alkyl groups, CN groups, heteroalkyl groups, aromaticgroups, heteroaromatic groups, a sulfone-containing group, (e.g.,CH₂SO₂CH₃, CH₂SO₂NH₂, NHSO₂CH₃, NCH₃SO₂CH₃, NHSO₂NHCH₃, NHSO₂CH₂CH₃,NHSO₂(CH₂)₂NH₂, NHSO₂N(CH₃)₂, NHSO₂(CH₂)₁₋₅CH₃, and NHSO₂(CH₂)₂NHCOCH₃),S, O, or N atoms, and combinations thereof.

In some embodiments, R1-R⁸ are independently selected from any of therespective substituents described herein or depicted in any of Tables1-8, in any combination. For example, in some embodiments, R¹-R⁸, whenpresent on a subscaffold, each independently comprise or consist of: H,alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane,butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane,2-methyl-hexane, 3-methyl, 2-propyl-octane, etc.), cycloalkyl (e.g.,cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane,etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane,propylcyclohexane, etc.)), a substituted alkyl group (e.g.,halogen-substituted alkyl group (e.g., mono-, di-, tetra-, penta- andtrihaloethane (e.g., trifluoroethane), halomethane (e.g.,fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane(e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol,etc.), alkylamine (e.g., primary amine (e.g., ethylamine,iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine,iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondaryamines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.),tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thiolkyl,combinations thereof, etc.), a substituted cycloalkyl group (e.g.,halogen-substituted cycloalkyl group, alkyl-substituted cycloalkylgroup, cycloalkoxy group, cyclolkylamine, etc.), a halogen (e.g., F, Cl,Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring (e.g.,heteroaryl), a substituted aromatic ring (e.g., branched aromatic ring(e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g.,chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring(e.g., comprising one or more nitrogen, oxygen and/or sulfur memberswhich may be non-substituted or substituted with alkyl, aryl, halogen,hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring(e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfurmembers), carbocyclic or heterocyclic aromatic ring comprising carbonatoms and one or more nitrogen, oxygen and/or sulfur members fused toanother aromatic ring (e.g., heteroaryl), a multi-ring system comprisinga combination of elements selected from aromatic rings, cycloalkane,heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/orhalogen-containing substituents (e.g., substituted heteroaryl), or ahydrogen bond donor or a hydrogen bond acceptor, and/or combinationsthereof.

In some embodiments, A comprises or consists of: C, N, O, or S; whereinwhen A comprises O or S, there is no further substitution at thatrespective position; wherein when A comprises N or C that respectiveposition is optionally substituted, wherein the substituent at thatrespective position comprises or consists of: alkyl group (e.g.,straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane,hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane,3-methyl, 2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane,cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branchedcyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane,propylcyclohexane, etc.)), a substituted alkyl group (e.g.,halogen-substituted alkyl group (e.g., trihaloethane (e.g.,trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane(e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.),alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primaryamine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine,iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine,etc.), secondary amines (e.g., dimethylamine, methylethanolamine,diphenylamine, etc.), tertiary amine (e.g., trimethylamine,triphenylamine, etc.), thiolkyl, combinations thereof, etc.), asubstituted cycloalkyl group (e.g., halogen-substituted cycloalkylgroup, cycloalkoxy group, acyclolkylamine, etc.), a halogen (e.g., F,Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, asubstituted aromatic ring (e.g., branched aromatic ring (e.g.,ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene,fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprisingone or more nitrogen, oxygen and/or sulfur members which may benon-substituted or substituted with alkyl, aryl, halogen, hydrogen bonddonor or acceptor, a heterocyclic non-aromatic ring (e.g., comprisingcarbon and one or more nitrogen, oxygen and/or sulfur members),carbocyclic or heterocyclic aromatic ring (e.g., heteroaryl) comprisingcarbon atoms and one or more nitrogen, oxygen and/or sulfur membersfused to another aromatic ring, a multi-ring system comprising acombination of elements selected from aromatic rings (e.g., heteroaryl),cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-,S-, and/or halogen-containing substituents, or a hydrogen bond donor ora hydrogen bond acceptor, and/or combinations thereof.

In some embodiments, B comprises or consists of: C, N, O, or S; whereinwhen B comprises O or S, there is no further substitution at thatrespective position; wherein when B comprises N or C that respectiveposition is optionally substituted, wherein the substituent at thatrespective position comprises or consists of: alkyl group (e.g.,straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane,hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane,3-methyl, 2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane,cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branchedcyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane,propylcyclohexane, etc.)), a substituted alkyl group (e.g.,halogen-substituted alkyl group (e.g., trihaloethane (e.g.,trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane(e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.),alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primaryamine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine,iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine,etc.), secondary amines (e.g., dimethylamine, methylethanolamine,diphenylamine, etc.), tertiary amine (e.g., trimethylamine,triphenylamine, etc.), thiolkyl, combinations thereof, etc.), asubstituted cycloalkyl group (e.g., halogen-substituted cycloalkylgroup, cycloalkoxy group, acyclolkylamine, etc.), a halogen (e.g., F,Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, asubstituted aromatic ring (e.g., branched aromatic ring (e.g.,ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene,fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprisingone or more nitrogen, oxygen and/or sulfur members which may benon-substituted or substituted with alkyl, aryl, halogen, hydrogen bonddonor or acceptor, a heterocyclic non-aromatic ring (e.g., comprisingcarbon and one or more nitrogen, oxygen and/or sulfur members),carbocyclic or heterocyclic aromatic ring (e.g., heteroaryl) comprisingcarbon atoms and one or more nitrogen, oxygen and/or sulfur membersfused to another aromatic ring, a multi-ring system comprising acombination of elements selected from aromatic rings (e.g., heteroaryl),cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-,S-, and/or halogen-containing substituents, or a hydrogen bond donor ora hydrogen bond acceptor, and/or combinations thereof.

In some embodiments, D comprises or consists of: C, N, O, or S; whereinwhen D comprises O or S, there is no further substitution at thatrespective position; wherein D comprises N or C that respective positionis optionally substituted, wherein the substituent at that respectiveposition comprises or consists of: alkyl group (e.g., straight-chainalkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.),branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane,cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl(e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), asubstituted alkyl group (e.g., halogen-substituted alkyl group (e.g.,trihaloethane (e.g., trifluoroethane), halomethane (e.g.,fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane(e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol,etc.), alkylamine (e.g., primary amine (e.g., ethylamine,iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine,iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondaryamines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.),tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thiolkyl,combinations thereof, etc.), a substituted cycloalkyl group (e.g.,halogen-substituted cycloalkyl group, cycloalkoxy group,acyclolkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), aketone, a carbocyclic ring, an aromatic ring, a substituted aromaticring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene,etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), aheterocyclic aromatic ring (e.g., comprising one or more nitrogen,oxygen and/or sulfur members which may be non-substituted or substitutedwith alkyl, aryl, halogen, hydrogen bond donor or acceptor, aheterocyclic non-aromatic ring (e.g., comprising carbon and one or morenitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclicaromatic ring (e.g., heteroaryl) comprising carbon atoms and one or morenitrogen, oxygen and/or sulfur members fused to another aromatic ring, amulti-ring system comprising a combination of elements selected fromaromatic rings (e.g., heteroaryl), cycloalkane, heterocyclic rings,alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containingsubstituents, or a hydrogen bond donor or a hydrogen bond acceptor,and/or combinations thereof.

In some embodiments, L is present or absent, and when present comprisesor consists of: wherein L is present or absent and comprises alkylene(e.g. methylene, —CH₂—, ethylene, —CH₂—CH₂—, etc) or oxalkylene (e.g.—O—, —CH₂—O—CH₂) groups.

In some embodiments, Q comprises or consists of: alkyl (C₁₋₅) orheteroalkyl with one or more N, O, or S atoms.

In some embodiments, Y comprises or consists of: O, S, N or C, andwherein when Y is N or C the Y position may be substituted with R^(a),with R^(a) consisting of or comprising an alkyl (e.g., branched (e.g.,isopropyl), straight chain (e.g., propyl), cycloalkyl (e.g.,cyclopropyl)), heteroalkyl (e.g., methyl propyl ether),alkyl-substituted aryl (e.g., ethylbenzene), substituted alkyl (e.g.,halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethylgroup), monohaloalkyl group (e.g. monofluoroethyl group), dihaloalkylgroup (e.g. difluoroethyl group), trihaloethyl group (e.g.,trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl ((CH₂)₂CF₃),trihalobutyl group (e.g., trifluorobutyl group ((CH₂)₃CF₃)),trihaloisopropyl (e.g., trifluoroisopropyl (See, e.g., compound 38)),1-fluoro,2-trifluoro, ethane (See, e.g., compound 21), 1-trifluoro,2-ethanol (See, e.g., compound 23)), alcohol (e.g., (CH₂)_(n)OH, whereinn=0-10), alkoxy (e.g., (CH₂)_(n)—OR, wherein n=0-10, wherein R is alkyl,(CH₂)_(n)-aryl, (CH₂)_(n)-aromatic, (CH₂)_(n)-heterocycle, substitutedor non-substituted aryl, aromatic or non-aromatic heterocycle with oneor more N, S, O, etc.), amino (e.g., alkyl amine, amino alkyl, etc.),cyano, sunlfonyl, methoxy, aldehyde, heterocycle, aromatic, combinationsthereof, etc.; and wherein L is present or absent and comprises alkylene(e.g. methylene, —CH₂—, ethylene, —CH₂—CH₂—, propylene, —CH₂—CH₂—CH₂—,etc) or oxalkylene (e.g. —O—, —CH₂—O—CH₂) groups.

In some embodiments, Z comprises or consists of: H, alkyl group (e.g.,straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane,hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane,3-methyl, 2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane,cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branchedcyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane,propylcyclohexane, etc.)), a substituted alkyl group (e.g.,halogen-substituted alkyl group (e.g., trihaloethane (e.g.,trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane(e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.),alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primaryamine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine,iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine,etc.), secondary amines (e.g., dimethylamine, methylethanolamine,diphenylamine, etc.), tertiary amine (e.g., trimethylamine,triphenylamine, etc.), thioalkyl, a substituted cycloalkyl group (e.g.,halogen-substituted cycloalkyl group, cycloalkoxy group,acyclolkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), aketone, a carbocyclic ring, an aromatic ring, a substituted aromaticring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene,etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), aheterocyclic aromatic ring (e.g., comprising one or more nitrogen,oxygen and/or sulfur members which may be non-substituted or substitutedwith alkyl, aryl, halogen, hydrogen bond donor or acceptor), aheterocyclic non-aromatic ring (e.g., comprising carbon and one or morenitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclicaromatic ring comprising carbon atoms and one or more nitrogen, oxygenand/or sulfur members fused to another aromatic ring, a multi-ringsystem comprising a combination of elements selected from aromaticrings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-,N-, O-, S-, and/or halogen-containing substituents, a hydrogen bonddonor or a hydrogen bond acceptor, a sulfur-containing group (e.g.,thiol, sulfide, disulfide, sulfoxide, sulfone), a group selected fromCHR⁴SO₂R⁵ or NR⁴SO₂R⁵, in which R⁴ comprises or consists of: H, alkylgroup (e.g., straight-chain alkyl (e.g., methane, ethane, propane,butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane,2-methyl-hexane, 3-methyl, 2-propyl-octane, etc.), cycloalkyl (e.g.,cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane,etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane,propylcyclohexane, etc.)), a substituted alkyl group (e.g.,halogen-substituted alkyl group (e.g., trihaloethane (e.g.,trifluoroethane), alkylnitrile group (e.g. ethanenitryle group, CH₂CN),alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primaryamine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine,iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine,etc.), secondary amines (e.g., dimethylamine, methylethanolamine,diphenylamine, etc.), tertiary amine (e.g., trimethylamine,triphenylamine, etc.), a carbocyclic ring, a substituted cycloalkylgroup (e.g., halogen-substituted cycloalkyl group, alkyl-substitutedcycloalkyl group, cycloalkoxy group, cyclolkylamine, etc.) and R⁵comprises or consists of: H, alkyl group (e.g., straight-chain alkyl(e.g., methane, ethane, propane, butane, pentane, hexane, etc.),branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane,cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl(e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), asubstituted alkyl group (e.g., halogen-substituted alkyl group (e.g.,trihaloethane (e.g., trifluoroethane), halomethane (e.g.,fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane(e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol,etc.), alkylamine (e.g., primary amine (e.g., ethylamine,iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine,iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondaryamines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.),tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl,a substituted cycloalkyl group (e.g., halogen-substituted cycloalkylgroup, cycloalkoxy group, acyclolkylamine, etc.), a ketone, acarbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g.,branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.),halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclicaromatic ring (e.g., comprising one or more nitrogen, oxygen and/orsulfur members which may be non-substituted or substituted with alkyl,aryl, halogen, hydrogen bond donor or acceptor), a heterocyclicnon-aromatic ring (e.g., comprising carbon and one or more nitrogen,oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ringcomprising carbon atoms and one or more nitrogen, oxygen and/or sulfurmembers fused to another aromatic ring, a multi-ring system comprising acombination of elements selected from aromatic rings, cycloalkane,heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/orhalogen-containing substituents, a hydrogen bond donor or a hydrogenbond acceptor, and/or combinations thereof, R⁵ might also be a part ofthe 3-8 member aromatic or non-aromatic ring comparising C, N, O, or S.

In some embodiments, the present invention provides methods for thetreatment of a disease or condition comprising: administering athienopyrimidine or thienopyridine class compound to a subject sufferingfrom said disease or condition. In some embodiments, thethienopyrimidine or thienopyridine class compounds comprise one ofsubscaffolds 1-6. In some embodiments, the thienopyrimidine orthienopyridine class compounds comprise one or compound 1-283. In someembodiments, the disease or condition comprises leukemia or a solidtumor cancer (e.g., breast cancer, prostate cancer, lung cancer, livercancer, pancreatic cancer, glioblastoma and melanoma, etc.). In someembodiments, the leukemia comprises acute leukemias, chronic leukemias,lymphoblastic leukemias, lymphocytic leukemias, myeloid leukemias,myelogenous leukemias, Acute lymphoblastic leukemia (ALL), Chroniclymphocytic leukemia (CLL), Acute myelogenous leukemia (AML), Chronicmyelogenous leukemia (CML), Hairy cell leukemia (HCL), T-cellprolymphocytic leukemia (T-PLL), Large granular lymphocytic leukemia,MLL-positive leukemias, MLL-induced leukemias, MLL-rearranged leukemias,etc.

In some embodiments, the present invention provides methods ofinhibiting the interaction of MLL (MLL1 and MLL2) and menin comprising:(a) providing: (i) a sample comprising MLL (or MLL fusion proteins) andmenin; and (ii) a thienopyrimidine and thienopyridine class compounds;(b) administering said composition to said sample; and (c) inhibitingthe interaction between said MLL and said menin, or said MLL fusionproteins and said menin. In some embodiments, the thienopyrimidine orthienopyridine class compounds comprises one of subscaffolds 1-6. Insome embodiments, the thienopyrimidine or thienopyridine class compoundcomprises one of compound 1-283.

The compositions may comprise combinations of any of the above compoundswith one another or with other compounds of interest. Stereoisomers,salts, and derivates of the compounds are further contemplated.

In some embodiments, the present invention provides a method comprisingadministering a composition for the treatment of leukemia (e.g., whichinhibits binding of one or more MLL fusion proteins to menin or MLL wildtype to menin) to a subject suffering from leukemia. In someembodiments, the leukemia comprises AML or ALL. In some embodiments, thecomposition comprises a thienopyrimidine or thienopyridine classcompound. In some embodiments, the composition comprises a compound ofthe general structure of one or subscaffolds 1, 2, 3, 4, 5, or 6. Insome embodiments, the composition comprises one of compounds 1-283and/or a derivative thereof.

In some embodiments, the present invention provides a method ofscreening compounds effective in treating leukemia comprising assayingone or more compounds for inhibition of the interaction between MLL andmenin. In some embodiments, the screening is performed in vitro. In someembodiments, the screening is performed in vivo. In some embodiments,the assaying comprises a fluorescence polarization assay. In someembodiments, the assaying comprises a time-resolved fluorescenceresonance energy transfer assay. In some embodiments, the assayingcomprises a nuclear magnetic resonance (NMR) methods. In someembodiments, the assaying comprises cellular assays and/or animal (e.g.,mice) studies.

In some embodiments, the present invention provides a method ofinhibiting the interaction of MLL and menin comprising: (a) providing:(i) a sample comprising MLL and menin and (ii) a composition configuredto inhibit the interaction of MLL and menin, (b) administering thecomposition to the sample, (c) contacting MLL and/or menin with thecomposition, and (d) inhibiting the interaction between MLL and menin,and between MLL fusion proteins and menin. In some embodiments, thesample comprises cells from a subject suffering from leukemia. In someembodiments, the subject is a human subject or a human patient. In someembodiments, the cells are within a subject suffering from leukemia. Insome embodiments, the composition comprises a thienopyrimidine andthienopyridine class compound. In some embodiments, the presentinvention comprises any structural derivatives of Compounds 1-283.

In some embodiments, the present invention provides methods comprisingthe use of a composition and/or compound described herein (e.g., aderivative of one of Subscaffolds 1-6, one of compounds 1-283, etc.). Insome embodiments, the present invention provides methods comprising theuse of a composition and/or compound described herein (e.g., aderivative of one of Subscaffolds 1-6, one of compounds 1-283, etc.) forthe treatment of leukemia.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Validation of direct binding of thienopyrimidine compounds tomenin: a) X-ray structure of menin in complex with compound 1; b)Isothermal Titration calorimetry (ITC) for binding of compound 1 tomenin.

FIG. 2. Co-Immunoprecipitation (co-IP) experiment performed in HEK293cells transfected with MLL-AF9 demonstrating inhibition of themenin-MLL-AF9 interaction in human cells by thienopyrimidine compounds:1, 108, 175.

FIG. 3. Thienopyrimidine compounds selectively inhibit proliferation ofMLL leukemia cells as shown in MTT cell viability assay performed forcompounds 1 and 108 (72 h incubation time) in MLL-AF9 transformed mousebone marrow cells (BMC) and in E2H-HLF transformed BMC, which were usedas a negative control cell line.

FIG. 4. Thienopyrimidine compounds inhibit growth of MLL-AF9 transformedBMC as demonstrated in the growth curves experiments.

FIG. 5. Growth curves experiments performed for compound 175 in MLL-AF9transformed BMC and Hoxa9/Meis1 transformed BMC (negative control cellline), showing great selectivity of the compound towards MLL fusionprotein transformed cells.

FIG. 6. Growth curves experiments performed for compound 175 in MLL-AF6and MLL-GAS7 transformed BMC.

FIG. 7. Compound 108 reduces colony number (left) and changes morphologyof colonies (right) as assessed in colony formation assay performed inMLL-AF9 BMC. Each round takes 7 days.

FIG. 8. Menin-MLL inhibitors induce differentiation in MLL-AF9 BMC asassessed by change in expression level of CD 11b differentiation marker(left) and change in cell morphology (right).

FIG. 9. Differentiation induced in MLL-AF9 BMC upon treatment withCompound 175: A. Change in expression level of CD11b, B. Change in cellmorphology.

FIG. 10. Menin-MLL inhibitors downregulate expression of downstreamtargets of MLL fusion proteins: Hoxa9 and Meis1. A. qRT-PCR performed inMLL-AF9 BMC for Compounds 1 and 108. B. qRT-PCR performed in MLL-AF9 BMCfor Compound 175.

FIG. 11. Menin-MLL inhibitors selectively inhibit growth of human MLLleukemia cell lines as shown by MTT cell viability assay performed forCompound 108 after 3 days of incubation in different human leukemia celllines.

FIG. 12. Thienopyrimidine compounds induce apoptosis (A) and cell cyclearrest (B) in human MLL leukemia cell lines (e.g. MV4;11 with MLL-AF4translocation).

FIG. 13. Thienopyrimidine compound 175 selectively inhibits growth ofhuman MLL leukemia cell lines (A) and has a limited effect in non-MLLleukemia cell lines (B).

FIG. 14. Thienopyrimidine compounds downregulate expression ofdownstream targets of MLL fusion proteins (Hoxa9 and Meis1) in human MLLleukemia cell lines.

FIG. 15. Thienopyrimidine compounds induce differentiation in human MLLleukemia cell lines: MV4;11 (A) and THP-1 (B).

FIG. 16. Pharmacokinetic (PK) profile of compound 108 after oral (p.o.)and intravenous (i.v.) injections of the compound to mice.

FIG. 17. MTD (Maximum Tolerated Dose) studies with compound 108 in miceafter i.p. (intraperitoneal) injections of the compound.

FIG. 18. In vivo efficacy studies with compound 108 in mice model ofMLL-AF9 leukemia. Increase in survival of leukemic mice was observedafter once daily i.p. injections of 75 mg/kg dose.

FIG. 19. PK profile in mice for compound 175 after i.p. and oraladministration of the compound.

DEFINITIONS

The nomenclature used herein for referring to substituents is eitherIUPAC format or a modified format in which functional groups within asubstituent are read in the order in which they branch from the scaffoldor main structure. For example, in the modified nomenclature,methyl-sulfonyl-propanol refers to CH₂SO₂CH₂CH₂CH₂OH or:

As another example, according to the modified nomenclature, amethyl-amine substituent is:

while an amino-methyl substituent is:

All chemical names of substituents should be interpreted in light ofIUPAC and/or the modified nomenclature and with reference to thechemical structures depicted and/or described herein.

The term “system” refers a group of objects, compounds, methods, and/ordevices that form a network for performing a desired objective.

As used herein a “sample” refers to anything capable of being subjectedto the compositions and methods provided herein. The sample may be invitro or in vivo. In some embodiments, samples are “mixture” samples,which samples from more than one subject or individual. In someembodiments, the methods provided herein comprise purifying or isolatingthe sample. In some embodiments, the sample is purified or unpurifiedprotein. In some embodiments, a sample may be from a clinical orresearch setting. In some embodiments, a sample may comprise cells,fluids (e.g. blood, urine, cytoplasm, etc.), tissues, organs, lysedcells, whole organisms, etc. In some embodiments, a sample may bederived from a subject. In some embodiments, a sample may comprise oneor more partial or whole subjects.

As used herein, the term “subject” refers to any animal including, butnot limited to, humans, non-human primates, bovines, equines, felines,canines, pigs, rodents (e.g., mice), and the like. The terms “subject”and “patient” may be used interchangeably, wherein the term “patient”generally refers to a human subject seeking or receiving treatment orpreventative measures from a clinician or health care provider.

As used herein, the terms “subject at risk for cancer” or “subject atrisk for leukemia” refer to a subject with one or more risk factors fordeveloping cancer and/or leukemia. Risk factors include, but are notlimited to, gender, age, genetic predisposition, environmental exposure,and previous incidents of cancer, preexisting non-cancer diseases, andlifestyle.

As used herein, the terms “characterizing cancer in subject”“characterizing leukemia in subject” refers to the identification of oneor more properties of a cancer and/or leukemia sample in a subject,including but not limited to, the presence of benign, pre-cancerous orcancerous tissue or cells and the stage of the cancer (e.g., leukemia).Cancers (e.g., leukemia) may be characterized by identifying cancercells with the compositions and methods of the present invention.

The terms “test compound” and “candidate compound” refer to any chemicalentity, pharmaceutical, drug, and the like that is a candidate for useto treat or prevent a disease, illness, sickness, or disorder of bodilyfunction (e.g., cancer). Test compounds comprise both known andpotential therapeutic compounds. A test compound can be determined to betherapeutic by screening using the screening methods of the presentinvention.

As used herein, the term “effective amount” refers to the amount of acompound (e.g., a compound having a structure presented above orelsewhere described herein) sufficient to effect beneficial or desiredresults. An effective amount can be administered in one or moreadministrations, applications or dosages and is not limited to orintended to be limited to a particular formulation or administrationroute.

As used herein, the term “co-administration” refers to theadministration of at least two agent(s) (e.g., a compound having astructure presented above or elsewhere described herein) or therapies toa subject. In some embodiments, the co-administration of two or moreagents/therapies is concurrent. In other embodiments, a firstagent/therapy is administered prior to a second agent/therapy. Those ofskill in the art understand that the formulations and/or routes ofadministration of the various agents/therapies used may vary. Theappropriate dosage for co-administration can be readily determined byone skilled in the art. In some embodiments, when agents/therapies areco-administered, the respective agents/therapies are administered atlower dosages than appropriate for their administration alone. Thus,co-administration is especially desirable in embodiments where theco-administration of the agents/therapies lowers the requisite dosage ofa known potentially harmful (e.g., toxic) agent(s).

As used herein, the term “pharmaceutical composition” refers to thecombination of an active agent with a carrier, inert or active, makingthe composition especially suitable for diagnostic or therapeutic use invivo, in vivo or ex vivo.

As used herein, the term “pharmaceutically acceptable carrier” refers toany of the standard pharmaceutical carriers, such as a phosphatebuffered saline solution, water, emulsions (e.g., such as an oil/wateror water/oil emulsions), and various types of wetting agents. Thecompositions also can include stabilizers and preservatives. Forexamples of carriers, stabilizers and adjuvants. (See e.g., Martin,Remington's Pharmaceutical Sciences, 15th Ed., Mack Publ. Co., Easton,Pa. [1975]).

As used herein, the term “pharmaceutically acceptable salt” refers toany pharmaceutically acceptable salt (e.g., acid or base) of a compoundof the present invention which, upon administration to a subject, iscapable of providing a compound of this invention or an activemetabolite or residue thereof. As is known to those of skill in the art,“salts” of the compounds of the present invention may be derived frominorganic or organic acids and bases. Examples of acids include, but arenot limited to, hydrochloric, hydrobromic, sulfuric, nitric, perchloric,fumaric, maleic, phosphoric, glycolic, lactic, salicylic, succinic,toluene-p-sulfonic, tartaric, acetic, citric, methanesulfonic,ethanesulfonic, formic, benzoic, malonic, naphthalene-2-sulfonic,benzenesulfonic acid, and the like. Other acids, such as oxalic, whilenot in themselves pharmaceutically acceptable, may be employed in thepreparation of salts useful as intermediates in obtaining the compoundsof the invention and their pharmaceutically acceptable acid additionsalts.

Examples of bases include, but are not limited to, alkali metals (e.g.,sodium) hydroxides, alkaline earth metals (e.g., magnesium), hydroxides,ammonia, and compounds of formula NW₄ ⁺, wherein W is C₁₋₄ alkyl, andthe like.

Examples of salts include, but are not limited to: acetate, adipate,alginate, aspartate, benzoate, benzenesulfonate, bisulfate, butyrate,citrate, camphorate, camphorsulfonate, cyclopentanepropionate,digluconate, dodecylsulfate, ethanesulfonate, fumarate, flucoheptanoate,glycerophosphate, hemisulfate, heptanoate, hexanoate, hydrochloride,hydrobromide, hydroiodide, 2-hydroxyethanesulfonate, lactate, maleate,methanesulfonate, 2-naphthalenesulfonate, nicotinate, oxalate, palmoate,pectinate, persulfate, phenylpropionate, picrate, pivalate, propionate,succinate, tartrate, thiocyanate, tosylate, undecanoate, and the like.Other examples of salts include anions of the compounds of the presentinvention compounded with a suitable cation such as Na⁺, NH₄ ⁺, and NW₄⁺ (wherein W is a C₁₋₄ alkyl group), and the like.

For therapeutic use, salts of the compounds of the present invention arecontemplated as being pharmaceutically acceptable. However, salts ofacids and bases that are non-pharmaceutically acceptable may also finduse, for example, in the preparation or purification of apharmaceutically acceptable compound.

As used herein, the term “instructions for administering said compoundto a subject,” and grammatical equivalents thereof, includesinstructions for using the compositions contained in a kit for thetreatment of conditions characterized by viral infection (e.g.,providing dosing, route of administration, decision trees for treatingphysicians for correlating patient-specific characteristics withtherapeutic courses of action). The compounds of the present invention(e.g. as shown in structures above and elsewhere presented herein) canbe packaged into a kit, which may include instructions for administeringthe compounds to a subject.

As used herein, the term “alkyl” refers to a moiety consisting of carbonand hydrogen containing no double or triple bonds. An alkyl may belinear, branched, cyclic, or a combination thereof, and may contain fromone to fifty carbon atoms. Examples of alkyl groups include but are notlimited to methyl, ethyl, propyl, isopropyl, cyclopropyl, butyl isomers(e.g. n-butyl, iso-butyl, tert-butyl, etc.) cyclobutyl isomers (e.g.cyclobutyl, methylcyclopropyl, etc.), pentyl isomers, cyclopentaneisomers, hexyl isomers, cyclohexane isomers, and the like. Unlessspecified otherwise (e.g., substituted alkyl group, heteroalkyl, alkoxygroup, haloalkyl, alkylamine, thioalkyl, etc.), an alkyl group containscarbon and hydrogen atoms only.

As used herein, the term “linear alkyl” refers to a chain of carbon andhydrogen atoms (e.g., ethane, propane, butane, pentane, hexane, etc.). Alinear alkyl group may be referred to by the designation —(CH₂)_(q)CH₃,where q is 0-49. The designation “C₁₋₁₂ alkyl” or a similar designation,refers to alkyl having from 1 to 12 carbon atoms such as methyl, ethyl,propyl isomers (e.g. n-propyl, isopropyl, etc.), butyl isomers,cyclobutyl isomers (e.g. cyclobutyl, methylcyclopropyl, etc.), pentylisomers, cyclopentyl isomers, hexyl isomers, cyclohexyl isomer, heptylisomers, cycloheptyl isomers, octyl isomers, cyclooctyl isomers, nonylisomers, cyclononyl isomers, decyl isomer, cyclodecyl isomers, etc.Similar designations refer to alkyl with a number of carbon atoms in adifferent range.

As used herein, the term “branched alkyl” refers to a chain of carbonand hydrogen atoms, without double or triple bonds, that contains afork, branch, and/or split in the chain (e.g.,3,5-dimethyl-2-ethylhexane, 2-methyl-pentane, 1-methyl-cyclobutane,ortho-diethyl-cyclohexane, etc.). “Branching” refers to the divergenceof a carbon chain, whereas “substitution” refers to the presence ofnon-carbon/non-hydrogen atoms in a moiety. Unless specified otherwise(e.g., substituted branched alkyl group, branched heteroalkyl, branchedalkoxy group, branched haloalkyl, branched alkylamine, branchedthioalkyl, etc.), a branched alkyl group contains carbon and hydrogenatoms only.

As used herein, the term “cycloalkyl” refers to a completely saturatedmono- or multi-cyclic hydrocarbon ring system. When composed of two ormore rings, the rings may be joined together in a fused, bridged orspiro-connected fashion. Cycloalkyl groups of the present applicationmay range from three to ten carbons (C₃ to C₁₀). A cycloalkyl group maybe unsubstituted, substituted, branched, and/or unbranched. Typicalcycloalkyl groups include, but are not limited to, cyclopropyl,cyclobutyl, cyclopentyl, cyclohexyl, and the like. If substituted, thesubstituent(s) may be an alkyl or selected from those indicated abovewith regard to substitution of an alkyl group unless otherwiseindicated. Unless specified otherwise (e.g., substituted cycloalkylgroup, heterocyclyl, cycloalkoxy group, halocycloalkyl, cycloalkylamine,thiocycloalkyl, etc.), an alkyl group contains carbon and hydrogen atomsonly.

As used herein, the term “heteroalkyl” refers to an alkyl group, asdefined herein, wherein one or more carbon atoms are independentlyreplaced by one or more heteroatoms (e.g., oxygen, sulfur, nitrogen,phosphorus, silicon, or combinations thereof). The alkyl groupcontaining the non-carbon substitution(s) may be a linear alkyl,branched alkyl, cycloalkyl (e.g., cycloheteroalkyl), or combinationsthereof. Non-carbons may be at terminal locations (e.g., 2-hexanol) orintegral to an alkyl group (e.g., diethyl ether).

As used herein, the term “substituted” (e.g., substituted alyklene)means that the referenced group (e.g., alkyl, aryl, etc.) comprises asubstituent group (e.g., carbon/hydrogen-only substituent,heterosubstituent, halosubstituent, etc.). The term “optionallysubstituted”, as used herein, means that the referenced group (e.g.,alkyl, cycloalkyl, etc.) may or may not be substituted with one or moreadditional group(s). Substituent groups may be selected from, but arenot limited to: alkyl, alkenyl, alkynyl, cycloalkyl, aryl, heteroaryl,heterocycloalkyl, hydroxyl, alkoxy, mercaptyl, cyano, halo, carbonyl,thiocarbonyl, isocyanato, thiocyanato, isothiocyanato, nitro,perhaloalkyl, perfluoroalkyl, and amino, including mono- anddi-substituted amino groups, and the protected derivatives thereof.Non-limiting examples of substituents include, halo, —CN, —OR, —C(O)R,—OC(O)R, —C(O)OR, OC(O)NHR, —C(O)N(R)₂, —SR—, —S(═O)R, —S(═O)₂R, —NHR,—N(R)₂, —NHC(O)—, NHC(O)O—, —C(O)NH—, S(═O)₂NHR, —S(O)₂N(R)₂, —NHS(═O)₂,—NHS(O)₂R, C¹-C⁶alkyl, C¹-C⁶alkoxy, aryl, heteroaryl, cycloalkyl,heterocycloalkyl, halo-substituted C¹-C⁶alkyl, halo-substitutedC¹-C⁶alkoxy, where each R is independently selected from H, halo,C¹-C⁶alkyl, C¹-C⁶alkoxy, aryl, heteroaryl, cycloalkyl, heterocycloalkyl,halo-substituted C¹-C⁶alkyl, halo-substituted C¹-C⁶alkoxy.

As used herein, the term “substituted alkyl” refers to an alkyl group,as defined herein, displaying one or more non-carbon-atom-containingmoieties (e.g., a group containing non-carbon atoms, possibly inaddition to carbon atoms). The non-carbon-atom-containing moieties atomsmay comprise: oxygen, sulfur, nitrogen, phosphorus, silicon, halogens(e.g. chlorine, bromine, flourine, iodine, etc.), or combinationsthereof). The non-carbon-atom-containing moieties may also comprisecarbon and hydrogen. The alkyl group containing the non-carbonsubstitution(s) may be a linear alkyl, branched alkyl, cycloalkyl (e.g.,cycloheteroalkyl), or combinations thereof. Examples of substituted alkygroups include: 2-hexanol, diethyl ether (also a heteroalkyl),1-chloro-propane, etc.

As used herein, the terms “heteroaryl” or “heteroaromatic” refer tomonocyclic, bicyclic, tricyclic, and other multicyclic ring systems(e.g., having four or greater ring members), wherein at least one ringin the system is aromatic, at least one ring in the system contains oneor more heteroatoms selected from nitrogen, oxygen and sulfur, andwherein each ring in the system contains 3 to 7 ring members. Unlessotherwise defined herein, suitable substituents on the unsaturatedcarbon atom of a heteroaryl group are generally selected from halogen;—R, —OR, —SR, —NO₂, —CN, —N(R)₂, —NRC(O)R, —NRC(S)R, —NRC(O)N(R)₂,—NRC(S)N(R)₂, —NRCO₂R, —NRNRC(O)R, —NRNRC(O)N(R)₂, —NRNRCO₂R,—C(O)C(O)R, —C(O)CH₂C(O)R, —CO₂R, —C(S)R, —C(O)N(R)₂, —C(S)N(R)₂,—OC(O)N(R)₂, —OC(O)R, —C(O)N(OR)R, —C(NOR)R, —S(O)₂R, —S(O)₃R,—SO₂N(R)₂, —S(O)R, —NRSO₂N(R)₂, —NRSO₂R, —N(OR)R, —C(═NH)—N(R)₂,—P(O)₂R, —PO(R)₂, —OPO(R)₂, —(CH₂)O₂NHC(O)R, phenyl (Ph) optionallysubstituted with R, —O(Ph) optionally substituted with R, —(CH₂)1-2(Ph),optionally substituted with R, or —CH═CH(Ph), optionally substitutedwith R, wherein each independent occurrence of R is selected fromhydrogen, optionally substituted C¹-C⁶alkyl, optionally substitutedC¹-C⁶alkoxy, an unsubstituted 5-6 membered heteroaryl, phenyl, —O(Ph),or —CH₂(Ph), or two independent occurrences of R, on the samesubstituent or different substituents, taken together with the atom(s)to which each R is bound, to form an optionally substituted 3-12membered saturated, partially unsaturated, or fully unsaturatedmonocyclic or bicyclic ring having 0-4 heteroatoms independentlyselected from nitrogen, oxygen, or sulfur. Non-limiting examples ofheteroaryl groups, as used herein, include benzofuranyl, benzofurazanyl,benzoxazolyl, benzopyranyl, benzthiazolyl, benzothienyl, benzazepinyl,benzimidazolyl, benzothiopyranyl, benzo[1,3]dioxole, benzo[b]furyl,benzo[b]thienyl, cinnolinyl, furazanyl, furyl, furopyridinyl,imidazolyl, indolyl, indolizinyl, indolin-2-one, indazolyl, isoindolyl,isoquinolinyl, isoxazolyl, isothiazolyl, 1,8-naphthyridinyl, oxazolyl,oxaindolyl, oxadiazolyl, pyrazolyl, pyrrolyl, phthalazinyl, pteridinyl,purinyl, pyridyl, pyridazinyl, pyrazinyl, pyrimidinyl, quinoxalinyl,quinolinyl, quinazolinyl, 4H-quinolizinyl, thiazolyl, thiadiazolyl,thienyl, triazinyl, triazolyl and tetrazolyl. Any substituents depictedin structures or examples herein, should be viewed as suitablesubstituents for use in embodiments of the present invention.

As used herein, the terms “heterocycloalkyl” of “heterocycle” refer to acycloalkyl, as defined herein, wherein one or more of the ring carbonsare replaced by a moiety selected from —O —, —N═, —NR—, —C(O)—, —S—,—S(O)— or —S(O)₂—, wherein R is hydrogen, C¹-C⁸alkyl or a nitrogenprotecting group, with the proviso that the ring of said group does notcontain two adjacent O or S atoms. Non-limiting examples ofheterocycloalkyl groups, as used herein, include morpholino,pyrrolidinyl, pyrrolidinyl-2-one, piperazinyl, piperidinyl,piperidinylone, 1,4-dioxa-8-aza-spiro[4.5]dec-8-yl, 2H-pyrrolyl,2-pyrrolinyl, 3-pyrrolinyl, 1,3-dioxolanyl, 2-imidazolinyl,imidazolidinyl, 2-pyrazolinyl, pyrazolidinyl, 1,4-dioxanyl,1,4-dithianyl, thiomorpholinyl, azepanyl, hexahydro-1,4-diazepinyl,tetrahydrofuranyl, dihydrofuranyl, tetrahydrothienyl, tetrahydropyranyl,dihydropyranyl, tetrahydrothiopyranyl, thioxanyl, azetidinyl, oxetanyl,thietanyl, oxepanyl, thiepanyl, 1,2,3,6-tetrahydropyridinyl, 2H-pyranyl,4H-pyranyl, dioxanyl, 1,3-dioxolanyl, dithianyl, dithiolanyl,dihydropyranyl, dihydrothienyl, dihydrofuranyl, imidazolinyl,imidazolidinyl, 3-azabicyclo[3.1.0]hexanyl, and3-azabicyclo[4.1.0]heptanyl.

DETAILED DESCRIPTION

The present invention provides thienopyrimidine and thienopyridine classcompounds. In certain embodiments, thienopyrimidine compounds areprovided for the treatment or prevention of one or more diseases orconditions (e.g., leukemia). Embodiments of the present inventiondirected toward the treatment and/or prevention of leukemia orrecurrence thereof are described herein; however, it should beunderstood that the compositions and methods described herein are notlimited to the leukemia application. Rather, in some embodiments, thecompositions and methods described herein should be understood to alsobe useful for the treatment and/or prevention of other cancers,including but not limited to breast, pancreastic, prostate and coloncancers, glioblastoma, diabetes etc. The compounds provided herein arenot limited to therapeutic uses; any additional uses for this class ofcompounds are also contemplated.

In some embodiments, thienopyrimidine and thienopyridine class compoundsof the present invention comprise a general formula of:

wherein W, X, Y, and R1-R4 independently comprise any suitablesubstituents described herein, or otherwise understood to one of skillin the art. In some embodiments, a thienopyrimidine class compound ofthe present invention comprises a general formula of one of:

In some embodiments, the R1-R8, A, B, D, Q, L, X, Y, and Z of the abovestructures each independently comprise or consist of one or anycombination of the following moieties:

-   Single atoms: H, Cl, Br, F, or I;-   Alkanes (alkyl groups): methane (methyl), ethane (ethyl), propane    (propyl), butane (butyl), pentane (pentyl), hexane (hexyl), or any    suitable straight chain or branched C¹-C²⁰ alkane;-   Alkenes: methene, ethene, propene, butene, pentene, hexene, or any    suitable C⁷-C²⁰ alkene;-   Alkynes: methyne, ethyne, propyne, butyne, pentyne, hexyne, or any    suitable C⁷-C²⁰ alkyne;-   Cycloalkanes: cyclopropane, cyclobutane, cyclopentane, cyclohexane,    or any suitable C⁷-C²⁰ cycloalkane;-   Aromatic rings (e.g., carbon-only or heteroaromatics (e.g.,    heteroaryl)): furan, benzofuran, isobenzofuran, pyrrole, indole,    isoindole, thiophene, benzothiophene, benzo[c]thiophene, imidazole,    benzimidazole, purine, pyrazole, indazole, oxazole, benzooxazole,    isoxazole, benzisoxazole, thiazole, benzothiazole, benzene,    napthalene, pyridine, quinolone, isoquinoline, pyrazine,    quinoxaline, pyrimidine, quinazoline, pyridazine, cinnoline,    phthalazine, triazine (e.g., 1,2,3-triazine; 1,2,4-triazine; 1,3,5    triazine), thiadiazole, etc.;-   Haloalkanes: halomethane (e.g., chloromethane, bromomethane,    fluoromethane, iodomethane), di- and trihalomethane (e.g.,    trichloromethane, tribromomethane, trifluoromethane,    triiodomethane), 1-haloethane, 2-haloethane, 1,2-dihaloethane,    1-halopropane, 2-halopropane, 3-halopropane, 1,2-dihalopropane,    1,3-dihalopropane, 2,3-dihalopropane, 1,2,3-trihalopropane, and any    other sutable combinations of alkanes (or substituted alkanes) an    halogens (e.g., Cl, Br, F, I, etc.);-   Alcohols: OH, methanol, ethanol, propanol, butanol, pentanol,    hexanol, cyclic alcohols (e.g., cyclohexanol), aromatic alcohols    (e.g., phenol), or any other suitable combination of an OH moiety    with a second moiety;-   Ketones: methyl methyl ketone (acetone), methyl ethyl ketone    (butanone), propyl ethyl ketone (pentanone)), or any other suitable    combination of alkyl chains with ═O;-   Aldehydes: methanal, ethanal, propanal, butanal, pentanal, hexanal,    or any other suitable combination of alkyl chain with ═O;-   Carboxylates: methanoate, ethanoate, propanote, butanoate,    pentanoate, hexanoate, or any other suitable combination of alkyl    chain with OO⁻;-   Carboxylic acids: methanoic acid, ethanoic acid, propanoic acid,    butanoic acid, pentanoic acid, hexanoic acid, or any other suitable    combination of alkyl chain with OOH;-   Ethers: methoxy, ethoxy, methylmethoxy, ethylmethoxy, or any other    suitable combination of alkyl chains surrounding an O;-   Amides: methanamide (CONH₂), ethanamide (CH₂CONH₂), propanamide    ((CH₂)₂CONH₂), alkan^(n)amide ((CH₂)_(n) CONH₂), n-methyl    alkan^(n)amide ((CH₂)_(n) CONHCH₃), c-methyl alkan^(n)amide    ((CH₂)_(n) NHCOCH₃), n-alkyl alkan^(n)amide ((CH₂)_(n)    CONH(CH₂)_(m)CH₃), c-methyl alkan^(n)amide ((CH₂)_(n)    NHCO(CH₂)_(m)CH₃), etc.;-   Primary amines: NH₂, methylamine, ethylamine, cyclopropylamine,    etc.;-   Secondary amines: aminomethyl (NHCH₃), aminoethyl (NHCH₂CH₃),    methyl-aminomethyl (CH₂NHCH₃; aka methylamine-methane),    alkyl^(n)-aminomethane ((CH₂)_(n) NHCH₃), etc.;-   Tertiary amines: dimethylamine (N(CH₃)₂), dimethylamine (N(CH₃)₂),    methyl-ethyl-amine (NCH₃CH₂CH₃), methane-diethylamine    (CH₂N(CH₂CH₃)₂; aka methylamine-diethane), etc.;-   Azides: methyl azide (CH₂NNN), ethyl azide ((CH₂)₂NNN), alkyl^(n)    azide ((CH₂)_(n) NNN), etc.-   Cyanates: methyl cyanate (CH₂OCN), ethyl cyanate ((CH₂)₂OCN),    alkyl^(n) cyanate ((CH₂)_(n) OCN), etc.-   Cyanos: methyl carbonitrile (CH₂CN), ethyl carbonitrile ((CH₂)₂CN),    alkyl^(n) carbonitrile ((CH₂)_(n) CN), etc.-   Thiols: methanethiol (CH₂SH), ethanethiol ((CH₂)₂SH),    alkan^(n)ethiol ((CH₂)_(n) SH), etc.-   Sulfides: dimethyl sulfide (CH₂SCH₃), methyl-ethyl sulfide    (CH₂SCH₂CH₃), alkyl^(n)-alkyl^(m) sulfide ((CH₂)_(n)    S(CH₂)_(m-1)CH₃), etc.;-   Sulfoxides: dimethyl sulfoxide (CH₂SOCH₃), methyl-ethyl sulfoxide    (CH₂SOCH₂CH₃), alkyl^(n)-alkyl^(m) sulfoxide ((CH₂)_(n)    SO(CH₂)_(m-1)CH₃), etc.;-   Sulfone: dimethyl sulfone (CH₂SO₂CH₃; aka methyl-sulfone-methyl),    methyl-ethyl sulfone (CH₂SO₂CH₂CH₃; aka methyl-sulfone-ethyl),    alkyl^(n)-alkyl^(m) sulfone ((CH₂)_(n)SO₂(CH₂)_(m-1)CH₃; aka    alkyl^(n)-sulfone-alkyl^(m)), R^(x)SO₂R^(y) (wherein Rx and Ry are    independently selected from any of the moieties provided in this    list or combinations thereof), etc.;-   Sulfinic acids: SO₂H, methyl sulfinic acid (CH₂SO₂H), ethyl sulfinic    acid ((CH₂)₂SO₂H), alkyl^(n)sulfinic acid ((CH₂)_(n) SO₂H), etc.;-   Thiocyanate: SCN, methyl thiocyanate (CH₂SCN), ethyl thiocyanate    ((CH₂)₂SCN), alkyl^(n)thiocyanate ((CH₂)nSCN), etc.;-   Phosphates: OP(═O)(OH)₂, methyl phosphate (CH₂OP(═O)(OH)₂), ethyl    phosphate ((CH₂)₂OP(═O)(OH)₂), alkyl^(n)phosphate    ((CH₂)_(n)OP(═O)(OH)₂), etc.

In various embodiments, the above listed moieties are attached at the X,Y, Z, A, B, D, and/or R positions in any suitable conformation. In someembodiments, the above listed functional groups are combined to producethe substituents depicted in compounds 1-283 of Tables 1-8.

TABLE 1 Examples of subscaffold 1 inhibitors of menin-MLL. LC-MS RT,compound min. or # Structure [MH]⁺ TLC R_(f) Inhibitors with IC50 0.01nM-0.1 μM  1

416.1 0.5  2

442.1 0.6 Inhibitors with IC50 0.1 uM-0.5 μM  3

427.3 1.71 min  4

399.1 1.13 min  5

437.2 2.03 min  6

581.2 2.51 min  7

469.3 2.78 min  8

469.3 2.22 min  9

399.0 1.64 min 10

455.1 0.5 11

385.5 1.42 min 12

535.2 0.6 13

487.2 0.3 14 AND Enantiomer 427.1 0.5

Inhibitors with IC50 0.5 μM-2 μM 15

419.2 1.89 min 16

401.2 1.51 min 17

511.3 2.56 min 18

483.4 1.89 min 19

469.3 2.50 min 20

439.0 2.30 min 21

473.2 2.48 min 22

23

471.5 1.93 min 24

491.0 2.73 min 25

406.5 1.25 min 26

452.0 1.87 min 27

28

413.0 2.01 min 29

327.5 1.42 min 30

376.5 1.42 min 31

359.5 1.61 min 32

415.6 2.07 min 33

415.6 2.09 min 34

429.4 2.26 min 35

438.2 0.6 36

402.2 0.6 37

452.2 0.6 38

430.1 0.7 39

483.2 0.6 40

466.2 0.6 41

505.2 0.6 42

491.1 0.6 LC-MS conditions: Column type: Phenomenex Kinetex 2.6u C18Column dimensions: 3.0 mm × 50 mm Temperature: 60° C. Solvent A: 0.1%TFA in water Solvent B: 0.1% TFA in MeCN Gradient program: 5% to 100%B/6 min UV wavelength: 254 nm TLC conditions: Plates: Pre-coated SilicaGel 60 F₂₅₄ Developing solvent: DCM:MeOH:NH₃•H₂O, 20:1:0.1

TABLE 2 Examples of subscaffold 2 inhibitors of menin-MLL. LC-MS RT,Compound min. or # Structure [MH]⁺ TLC R_(f) Inhibitors with IC50 0.01nM-0.1 μM 43

513.1 0.4 44

514.1 0.2 45

514.3 1.76 min 46

528.1 1.70 min 47

515.2 1.44 min 48

529.0 1.69 min 49

528.1 1.85 min 50

543.4 1.57 min 51

543.4 1.90 min 52

583.0 2.04 min 53

585.1 1.73 min 54

556.3 1.99 min 55

598.0 1.52 min 56

542.2 1.82 min 57

585.1 1.57 min 58

556.9 1.43 min 59

571.3 1.45 min 60

585.1 1.51 min 61

553.0 1.77 min 62

625.4 1.74 min 63

587.0 2.15 min 64

547.9 2.02 min 65

562.0 2.07 min 66

576.1 2.13 min Inhibitors with IC50 0.1 μM-0.5 μM 67

421.1 0.6 68

437.1 0.5 69

436.1 0.5 70

455.1 0.6 71

455.1 0.6 72

439.1 0.6 73

439.1 0.6 74

451.1 0.5 75

439.1 0.6 76

501.2 0.6 77

460.1 0.5 78

532.1 0.2 79

567.1 0.4 80

504.1 1.50 min 81

460.0 1.76 min 82

514.3 1.60 min 83

580.0 1.71 min 84

605.3 1.90 min 85

596.3 2.23 min Inhibitors with IC50 0.5 μM-2 μM 86

400.1 0.4 87

413.2 0.5 88

435.1 0.6 89

427.2 0.6 90

441.2 0.6 91

414.2 0.4 92

451.1 0.5 93

449.2 0.6 94

451.1 0.5 95

451.1 0.5 96

514.1 0.2 97

540.1 0.2 98

555.2 0.4 99

504.4 1.60 min 100 

596.3 2.26 min 101 

570.1 2.11 min 102 

568.3 2.10 min 103 

556.0 1.99 min 104 

589.1 2.30 min

TABLE 3 Examples of subscaffold 3 inhibitors of menin-MLL. LC-MS RT,min. or Compound # Structure [MH]⁺ TLC R_(f) Inhibitors with IC50 0.01nM-0.1 μM 105

423.1458 0.3 106

472.31  1.46 min Inhibitors with IC50 0.1 uM-0.5 μM 107

453.1   1.25 min 108

407.5   1.72 min 109

423.1   1.31 min 110

437.2   1.32 min 111

439.3   1.28 min 112

437.2   1.31 min 113

422.2   1.61 min 114

423.2   1.30 min 115

526.3   1.59 min 116

504.1   1.47 min 117

421.0   1.55 min 118

435.4   2.06 min 119

441.1   1.76 min 120

435.5   1.59 min 121

436.3   1.12 min 122

457.3   1.65 min 123

422.1618 0.2 124

512.2093 0.4 125

466.1885 0.1 126

420.7   1.47 min 127

465.2   0.1 128

481.1   0.1 129

451.1   0.3 130

464.2   1.32 min 131

396.1   1.25 min 132

413.5   1.37 min 133

413.5   1.37 min 134

396.1459 0.3 135

433.3   1.62 min Inhibitors with IC50 0.5 μM-2 μM 136

476.2   1.35 min 137

436.3   1.05 min 138

433.3   1.15 min 139

422.2   1.01 min 140

437.2   1.16 min 141

473.2   1.57 min 142

520.3   1.41 min 143

519.4    1.28 144

145

146

475.0   1.72 min 147

421.3   1.95 min 148

475.0   1.54 min 149

367.0   1.29 min 150

381.5   1.42 min 151

381.5   1.46 min 152

447.0   1.44 min 153

381.5   1.42 min 154

155

403.6   1.35 min 156

486.4   1.49 min 157

422.1629 0.3 158

434.1630 0.2 159

472.3   1.51 min

TABLE 4 Examples of subscaffold 3 and 4 inhibitors of menin-MLL. LC-MSRT, min. or Compound # Structure [MH]⁺ TLC R_(f) Inhibitors with IC500.01 nM-0.1 μM 160

486.1676 0.2 161

597.2367 0.2 162

540.2159 0.3 163

501.1   1.91 min 164

501.1   1.94 min Inhibitors with IC50 0.1 μM-0.5 μM 165

423.1458 0.2 166

422.1625 0.2 167

512.2095 0.3 168

526.2243 0.3 169

504.2400 0.3 170

533.2310 0.3 171

518.2557 0.3 172

583.2127 0.3 173

583.2133 0.3 174

512.1974 0.3

TABLE 5 Examples of subscaffold 4 inhibitors of menin-MLL. LC-MS RT,min. or Compound # Structure [MH]⁺ TLC R_(f) Inhibitors with IC50 0.01nM-0.1 μM 175

471.1579 0.3 176

489.1485 0.3 177

499.1891 0.4 178

525.2052 0.4 179

515.1828 0.2 180

501.1684 0.3 181

501.1675 0.3 182

487.1519 0.3 183

501.1678 0.2 184

489.4   1.60 min 185

551.2   1.23 min 186

514.1998 0.1 187

545.1951 0.2 188

545.1941 0.2 189

528.1783 0.2 190

559.2098 0.2 191

559.2096 0.2 192

584.2415  0.15 193

558.123  0.1 194

542.5   1.33 min 195

552.4   1.55 min 196

565.3   1.63 min 197

510.4   1.65 min 198

553.6   1.63 min 199

551.8   1.65 min 200

568.3   1.73 min 201

582.1   1.80 min 202

551.2   1.55 min 203

565.3   1.31 min 204

552.4   1.52 min 205

546.1   1.48 min 206

471.1576 0.4 207

566.5   1.53 min 208

556.0   1.46 min 209

566.2   1.52 min 210

564.4   1.43 min 211

501.1   1.77 min 212

541.9   1.82 min 213

546.1690 0.1 214

546.1693 0.1 215

515.1835 0.2 216

572.2050 0.1 217

589.2204 0.1 218

485.2   2.10 min 219

485.2   2.02 min 220

546.2   1.86 min 221

559.0   1.82 min 222

585.1   1.72 min 223

581.2   2.12 min 224

505.1181 0.3 225

562.1400 0.1 226

579.1552 0.1 Inhibitors with IC50 0.1 μM-0.5 μM 227

446.2   1.53 min 228

471.1584 0.3 229

471.1579 0.3 230

486.1675 0.2 231

500.1844 0.3 232

489.1685 0.2 233

486.1679 0.3 234

489.1483 0.3 235

487.1517 0.3 236

524.8   1.45 min 237

559.3   1.57 min 238

584.2   1.52 min 239

556.3 1.52 min 240

553.3   1.52 min 241

580.3   1.81 min 242

476.1729 0.2 243

446.2   1.52 min 244

515.2   1.98 min 245

489.1   1.96 min 246

546.1   1.77 min 247

542.1945 0.1 Inhibitors with IC50 0.5 μM-2 μM 248

473.2   1.47 min 249

472.3   1.39 min 250

463.3    1.14 251

586.4   1.27 min 252

485.1735 0.3

TABLE 6 Examples of subscaffold 5 inhibitors of menin-MLL. CompoundLC-MS RT, # Structure [MH]⁺ min. or R_(f) Inhibitors with IC50 0.1μM-0.5 μM 253

534.1 1.20 min 254

489.1 1.63 min 255

504.4 1.52 min 256

480.1 1.65 min 257

485.2 1.67 min 258

435.4 1.49 min 259

540.4 1.57 min 260

455.2 1.54 min 261

455.2 1.59 min 262

500.2 1.45 min 263

446.2 1.62 min Inhibitors with IC50 0.5 μM-2 μM 264

502.3 1.77 min 265

450.4 1.09 min 266

451.3 1.15 min 267

533.5 1.26 min 268

523.6 1.68 min 269

523.3 2.00 min 270

463.0 1.76 min 271

505.3 1.70 min 272

520.3 1.19 min 273

451.3 1.50 min 274

489.5 1.49 min 275

435.4 1.79 min 276

489.5 1.58 min 277

421.0 1.27 min

TABLE 7 Examples of subscaffold 3 and 4 inhibitors of menin-MLL. LC-MSRT, Compound min. or # Structure [MH]⁺ TLC R_(f) Inhibitors with IC500.01 nM-0.1 μM 278

500.2 1.45 min 279

431.2 1.78 min 280

436.0 1.19 min Inhibitors with IC50 0.1 μM-0.5 μM 281

450.1 1.30 min Inhibitors with IC50 0.5 μM-2 μM 282

366.3 1.35 min

TABLE 8 Examples of subscaffold 6 inhibitors of menin-MLL. LC-MS RT,Compound min. or # Structure [MH]⁺ TLC R_(f) Inhibitors with IC₅₀ 0.01nM-0.1 μM 283

407.2 1.51 minIn other embodiments, additional substituents, not depicted in Tables1-8 or described herein by name or formula, are formed by combination ofthe above functional groups; such substituents are within the scope ofthe present invention, and may be appended to one or more ofsubscaffolds 1-6 to yield compositions within the scope of the presentinvention.

Subscaffolds 1-6 are provided herein as exemplary subscaffolds of thegeneral thienopyrimidine and thienopyridine class of compounds. Whilethese subscaffolds, with any combination of the substituents depicted ordescribed herein (e.g., explicitly or through combination of functionalgroups), are within the scope of embodiments of the invention, thepresent invention is not limited to such subscaffolds. Thienopyrimidineand thienopyridine derivatives of subscaffolds 1-6 are also within thescope of embodiments of the present invention. Substitutions and/oraddition/deletion of substituents of subscaffolds 1-6 that producefunctional equivalents and/or improved functionality (e.g., enhancedtherapeutic effect, enhanced bioavailability, improved human tolerance,reduced side effects, etc.) are also within the scope of embodiments ofthe present invention.

In some embodiments, the present invention provides compositions andmethods for prevention and/or treatment of leukemia (e.g. MLL-relatedleukemia and other acute leukemias). In some embodiments, the presentinvention provides compositions and method for the inhibition of theprotein-protein interaction between menin and MLL fusion proteins and/ormenin and MLL wild type proteins (both MLL1 and MLL2). In someembodiments, compositions and methods inhibit the interaction that isimportant for the oncogenic (e.g. leukemogenic) potential of MLLfusions. In some embodiments, the present invention provides smallmolecule inhibitors of interactions between menin and MLL fusionproteins and/or menin and MLL wild type proteins (both MLL1 and MLL2).In some embodiments, compositions and methods reverse (e.g. inhibit,decrease, abolish, etc.) the oncogenic (e.g. leukemogenic) potential ofMLL fusion proteins. In some embodiments, compositions find utility intargeted therapies (e.g. anti-leukemia agents). In some embodiments,compounds block menin-MLL interactions.

In some embodiments, the present invention provides compositions whichinhibit the interaction between MLL (e.g. MLL fusion proteins and MLLwild type) and menin. In some embodiments, any compounds, smallmolecules (e.g. pharmaceuticals, drugs, drug-like molecules, etc.),macromolecules (e.g. peptides, nucleic acids, etc.) and/ormacromolecular complexes which inhibit the MLL-menin interaction findutility in the present invention. In some embodiments, the presentinvention provides small molecule compounds which inhibit MLL-menininteractions. In some embodiments, compositions of the present inventiondecrease the affinity of menin for MLL (e.g. MLL fusion proteins) and/orMLL (e.g. MLL wild type protein) for menin. In some embodiments,compositions of the present invention disrupt bonding (e.g. hydrogenbonding, ionic bonding, covalent bonding, etc.), molecular interactions(e.g. hydrophobic interactions, electrostatic interactions, van derWaals interactions, etc.), shape recognition, and/or molecularrecognition between MLL (e.g. MLL fusion proteins or MLL wild typeprotein) and menin. However, an understanding of the mechanisms ofaction is not required to practice the invention and the invention isnot limited to any particular mechanism of action.

The present invention provides any small molecules or classes of smallmolecules which disrupt, target, or inhibit MLL/menin interactions;and/or treat/prevent leukemia. In some embodiments, small molecules areeffective in inhibiting the interaction of MLL-fusion proteins withmenin or MLL wild type protein with menin. In particular embodiments,the present invention provides thienopyrimidine and thienopyridineclasses of small molecules. In some embodiments, thienopyrimidine smallmolecules of the present invention inhibit the interaction of MLL (e.g.MLL-fusion proteins or MLL wild type, both MLL1 and MLL2) with menin. Insome embodiments, thienopyrimidine and thienopyridine small molecules ofthe present invention inhibit the oncogenic (e.g. leukemogenic) effectsof MLL-fusion proteins, and/or MLL-menin and MLL fusion protein-menininteractions. In some embodiments, thienopyrimidine and thienopyridinesmall molecules of the present invention treat and/or prevent leukemia(e.g. MLL-dependant leukemias, MLL-related leukemias, or other leukemiaswith and without high level of HOX genes expression etc.).

In some embodiments, the present invention provides administration ofcompositions of the present invention to subjects (e.g. leukemiapatients) to treat or prevent disease (e.g. cancer, leukemia,MLL-related leukemia, etc.). In some embodiments, the present inventionprovides administration of compositions for the treatment or preventionof leukemia (e.g. acute leukemias, chronic leukemias, lymphoblasticleukemias, lymphocytic leukemias, myeloid leukemias, myelogenousleukemias, Acute lymphoblastic leukemia (ALL), Chronic lymphocyticleukemia (CLL), Acute myelogenous leukemia (AML), Chronic myelogenousleukemia (CML), Hairy cell leukemia (HCL), T-cell prolymphocyticleukemia (T-PLL), Large granular lymphocytic leukemia, MLL-positiveleukemias, MLL-induced leukemias, etc.).

In some embodiments, any of the above compounds is co-administered orused in combination with a known therapeutic agent (e.g., methotrexate,6-mercaptopurine, antibody therapies, etc.). In some embodiments, acompound of the present invention is co-administered with anothertherapeutic agent effective in treating one or more leukemias.

In some embodiments, a compound of the present invention isco-administered with one or more therapeutic agents approved for thetreatment of Acute Lymphoblastic Leukemia (ALL), for example: ABITREXATE(Methotrexate), ADRIAMYCIN PFS (Doxorubicin Hydrochloride), ADRIAMYCINRDF (Doxorubicin Hydrochloride), ARRANON (Nelarabine), AsparaginaseErwinia chrysanthemi, CERUBIDINE (Daunorubicin Hydrochloride), CLAFEN(Cyclophosphamide), CLOFARABINE, CLOFAREX (Clofarabine), CLOLAR(Clofarabine), Cyclophosphamide, Cytarabine, CYTOSAR-U (Cytarabine),CYTOXAN (Cyclophosphamide), Dasatinib, Daunorubicin Hydrochloride,Doxorubicin Hydrochloride, Erwinaze (Asparaginase Erwinia Chrysanthemi),FOLEX (Methotrexate), FOLEX PFS (Methotrexate), GLEEVEC (ImatinibMesylate), ICLUSIG (Ponatinib Hydrochloride), Imatinib Mesylate, MARQIBO(Vincristine Sulfate Liposome), Methotrexate, METHOTREXATE LPF(Methorexate), MEXATE (Methotrexate), MEXATE-AQ (Methotrexate),Nelarabine, NEOSAR (Cyclophosphamide), ONCASPAR (Pegaspargase),Pegaspargase, Ponatinib Hydrochloride, RUBIDOMYCIN (DaunorubicinHydrochloride), SPRYCEL (Dasatinib), TARABINE PFS (Cytarabine), VINCASARPFS (Vincristine Sulfate), Vincristine Sulfate, etc.

In some embodiments, a compound of the present invention isco-administered with one or more therapeutic agents approved for thetreatment of Acute Myeloid Leukemia (AML), for example: ADRIAMYCIN PFS(Doxorubicin Hydrochloride), ADRIAMYCIN RDF (Doxorubicin Hydrochloride),Arsenic Trioxide, CERUBIDINE (Daunorubicin Hydrochloride), CLAFEN(Cyclophosphamide), Cyclophosphamide, Cytarabine, CYTOSAR-U(Cytarabine), CYTOXAN (Cyclophosphamide), Daunorubicin Hydrochloride,Doxorubicin Hydrochloride, NEOSAR (Cyclophosphamide), RUBIDOMYCIN(Daunorubicin Hydrochloride), TARABINE PFS (Cytarabine), TRISENOX(Arsenic Trioxide), VINCASAR PFS (Vincristine Sulfate), VincristineSulfate, etc.

In some embodiments, a compound of the present invention isco-administered with one or more therapeutic agents approved for thetreatment of Chronic Lymphocytic Leukemia (CLL), for example:Alemtuzumab, AMBOCHLORIN (Chlorambucil), AMBOCLORIN (Chlorambucil),ARZERRA (Ofatumumab), Bendamustine Hydrochloride, CAMPATH (Alemtuzumab),CHLORAMBUCILCLAFEN (Cyclophosphamide), Cyclophosphamide, CYTOXAN(Cyclophosphamide), FLUDARA (Fludarabine Phosphate), FludarabinePhosphate, LEUKERAN (Chlorambucil), LINFOLIZIN (Chlorambucil), NEOSAR(Cyclophosphamide), Ofatumumab, TREANDA (Bendamustine Hydrochloride),etc.

In some embodiments, a compound of the present invention isco-administered with one or more therapeutic agents approved for thetreatment of Chronic Myelogenous Leukemia (CML), for example: BOSULIF(Bosutinib), Bosutinib, CLAFEN (Cyclophosphamide), Cyclophosphamide,Cytarabine, CYTOSAR-U (Cytarabine), CYTOXAN (Cyclophosphamide),Dasatinib, GLEEVEC (Imatinib Mesylate), ICLUSIG (PonatinibHydrochloride), Imatinib Mesylate, NEOSAR (Cyclophosphamide), Nilotinib,Omacetaxine Mepesuccinate, Ponatinib Hydrochloride, SPRYCEL (Dasatinib),SYNRIBO (Omacetaxine Mepesuccinate), TARABINE PFS (Cytarabine), TASIGNA(Nilotinib), etc.

In some embodiments, a compound of the present invention isco-administered with one or more therapeutic agents approved for thetreatment of Meningeal Leukemia, for example: CYTARABINE, CYTOSAR-U(Cytarabine), TARABINE PFS (Cytarabine), etc.

In some embodiments, the compositions of the present invention areprovided as pharmaceutical and/or therapeutic compositions. Thepharmaceutical and/or therapeutic compositions of the present inventioncan be administered in a number of ways depending upon whether local orsystemic treatment is desired and upon the area to be treated.Administration can be topical (including ophthalmic and to mucousmembranes including vaginal and rectal delivery), pulmonary (e.g., byinhalation or insufflation of powders or aerosols, including bynebulizer; intratracheal, intranasal, epidermal and transdermal), oralor parenteral. Parenteral administration includes intravenous,intraarterial, subcutaneous, intraperitoneal or intramuscular injectionor infusion; or intracranial, e.g., intrathecal or intraventricular,administration. Compositions and formulations for topical administrationcan include transdermal patches, ointments, lotions, creams, gels,drops, suppositories, sprays, liquids and powders. Conventionalcarriers; aqueous, powder, or oily bases; thickeners; and the like canbe necessary or desirable. Compositions and formulations for oraladministration include powders or granules, suspensions or solutions inwater or non aqueous media, capsules, sachets or tablets. Thickeners,flavoring agents, diluents, emulsifiers, dispersing aids or binders canbe desirable. Compositions and formulations for parenteral, intrathecalor intraventricular administration can include sterile aqueous solutionsthat can also contain buffers, diluents and other suitable additivessuch as, but not limited to, penetration enhancers, carrier compoundsand other pharmaceutically acceptable carriers or excipients.Pharmaceutical and/or therapeutic compositions of the present inventioninclude, but are not limited to, solutions, emulsions, and liposomecontaining formulations. These compositions can be generated from avariety of components that include, but are not limited to, preformedliquids, self emulsifying solids and self emulsifying semisolids.

The pharmaceutical and/or therapeutic formulations of the presentinvention, which can conveniently be presented in unit dosage form, canbe prepared according to conventional techniques well known in thepharmaceutical/nutriceutical industries. Such techniques include thestep of bringing into association the active ingredients with thepharmaceutical carrier(s) or excipient(s). In general the formulationsare prepared by uniformly and intimately bringing into association theactive ingredients with liquid carriers or finely divided solid carriersor both, and then, if necessary, shaping the product. The compositionsof the present invention can be formulated into any of many possibledosage forms such as, but not limited to, tablets, capsules, liquidsyrups, soft gels, suppositories, and enemas. The compositions of thepresent invention can also be formulated as suspensions in aqueous, nonaqueous, oil-based, or mixed media. Suspensions can further containsubstances that increase the viscosity of the suspension including, forexample, sodium carboxymethylcellulose, sorbitol and/or dextran. Thesuspension can also contain stabilizers. In one embodiment of thepresent invention the pharmaceutical compositions can be formulated andused as foams. Pharmaceutical foams include formulations such as, butnot limited to, emulsions, microemulsions, creams, jellies andliposomes. While basically similar in nature these formulations vary inthe components and the consistency of the final product.

Dosing and administration regimes are tailored by the clinician, orothers skilled in the pharmacological arts, based upon well knownpharmacological and therapeutic considerations including, but notlimited to, the desired level of therapeutic effect, and the practicallevel of therapeutic effect obtainable. Generally, it is advisable tofollow well-known pharmacological principles for administratingchemotherapeutic agents (e.g., it is generally advisable to not changedosages by more than 50% at time and no more than every 3-4 agenthalf-lives). For compositions that have relatively little or nodose-related toxicity considerations, and where maximum efficacy isdesired, doses in excess of the average required dose are not uncommon.This approach to dosing is commonly referred to as the “maximal dose”strategy. In certain embodiments, the compounds are administered to asubject at a dose of about 0.01 mg/kg to about 200 mg/kg, morepreferably at about 0.1 mg/kg to about 100 mg/kg, even more preferablyat about 0.5 mg/kg to about 50 mg/kg. When the compounds describedherein are co-administered with another agent (e.g., as sensitizingagents), the effective amount may be less than when the agent is usedalone. Dosing may be once per day or multiple times per day for one ormore consecutive days.

EXPERIMENTAL Example 1 General Methods of Compounds Synthesis

Compounds of Subscaffold 1 can be prepared according to the followinggeneral methods (Scheme 1 and 2).

Compounds of Subscaffold 2 can be prepared according to the followinggeneral methods (Scheme 3 and 4).

Compounds of Subscaffold 3 can be prepared according to the followinggeneral methods (Scheme 5 and 6).

Compounds of Subscaffold 4 can be prepared according to the followinggeneral methods (Scheme 7 and 8).

Compounds of Subscaffold 5 can be prepared according to the followinggeneral methods (Scheme 9 and 10).

Compounds of Subscaffold 6 can be prepared according to the followinggeneral methods (Scheme 11 and 12).

Example 2 Representative Procedure for the Synthesis of Compounds fromSubscaffold 1

4,4,4-trifluorobuteraldehyde 5 g (39.6 mmol), cyanoacetamide 3.36 g(39.6 mmol) and sulfur 1.28 g (39.6 mmol) was stirred in 40 mL of DMF inthe presence of 6.7 mL of triethylamine for 24 hs. Solvent wasevaporated under reduced pressure and the residue was loaded on silicagel column and eluted with pure ethyl acetate to afford 8.4 g of2-amino-5-(2,2,2-trifluoroethyl)thiophene-3-carboxamide. ¹H NMR CDCl₃(300 MHz): 7.97 (s, 1H), 6.76 (s, 1H), 3.59 (br, 2H), 3.35 (q, 2H, J10.3 Hz), 2.98 (s, 1H), 2.88 (s, 1H). ¹³C NMR CDCl₃ (75 MHz): 168.6,125.6, 124.3, 111.7, 107.3, 36.8, 34.7 (q, J 31.4 Hz).

8.4 g of 2-amino-5-(2,2,2-trifluoroethyl)thiophene-3-carboxamide wasrefluxed in a mixture of 28 mL of triethylorthoformate and 20 mL ofacetic acid for 4 hs. Solvents were removed under reduced pressure andthe residue was triturated hexane-ethyl acetate mixture (1:1). The solidwas filtered off to afford 5.7 g of6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4(3H)-one. ¹H NMR MeOH-d4(300 MHz): 12.6 (br, 1H), 8.14 (s, 1H), 7.42 (s, 1H), 4.07 (q, 2H, J11.0 Hz). ¹³C NMR MeOH-d4 (75 MHz): 164.5, 157.01, 146.1, 128.4, 124.6,123.5, 33.6 (q, J 31.5 Hz).

5.7 g of 6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4(3H)-one wasadded to 16 mL of POCl₃ with one drop of DMF. The heterogeneous mixturewas refluxed for 3 hs and then evaporated. The residue was quenched withice and saturated ammonia solution and extracted with chloroform.Combined extracts were evaporated with silica gel and loaded on a shortsilica gel column. The column was eluted with hexane-ethyl acetate (5:1)to afford 5.9 g of4-chloro-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine. ¹H NMR CDCl₃(300 MHz): 8.86 (s, 1H), 7.39 (s, 1H), 3.76 (q, 2H, J 9.9 Hz). ¹³C NMRCDCl₃ (75 MHz): 169.0, 154.7, 153.2, 129.9, 125.3, 123.5, 121.3, 35.9(q, J 33.0 Hz).

0.5 g of 3-isothiocyanato-2-methylprop-1-ene was added to dropwise viasyringe to a solution of 1-Bocpiperazine in 5 mL of ethanol. The mixturewas stirred for 1.5 hs at RT and then evaporated. The residue was washedseveral times with diethyl ether to produce 1.1 g of white solidintermediate, which was dissolved in 3 mL of conc. HCl and heated in thepressure tube at 100 degrees for 1.5 hours. Cooled solution was quenchedwith ammonia solution and extracted with ethyl acetate. Combined organiclayers were washed with brine, dried over MgSO₄ and evaporated to affordpure 382 mg of 5,5-dimethyl-2-(piperazin-1-yl)-2,5-dihydrothiazole,which was use as is in the next step. ¹H NMR (400 MHz, CDCl₃): δ 1.53(6H, s), 2.96 (4H, t, J=5 Hz), 3.49 (4H, t, J=5 Hz), 3.73 (2H, s). ¹³CNMR (100 MHz, CDCl₃): δC 28.83 (2C), 45.76 (2C), 49.34 (2C), 59.52,73.30, 164.16; mp 67° C.-70° C.; Mass spec (ES+): m/z 199.2 (M⁺+1).

A solution of 0.5 g of4-chloro-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine (2.4 mmol),0.56 g of 5,5-dimethyl-2-(piperazin-1-yl)-2,5-dihydrothiazole (2.8mmol), and 0.91 g of N,N-diisopropylethylamine (7.1 mmol) in 20 mL ofTHF was refluxed for 6 h. After cooling, the mixture was partitionedbetween ethyl acetate and H₂O. The combined organic extracts were washedwith brine, dried over MgSO₄ and concentrated to a pale yellow solid.Purification by silica gel column chromatography usingdichloromethane/methanol (97:3) as eluent gave 0.82 g of4-(4-(5,5-dimethyl-4,5-dihydrothiazol-2-yl)piperazin-1-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine(compound 1) as a pale yellow solid. Its monohydrochloride salt wasobtained by adding 1 equivalent of 1N HCl solution in diethyl ether to asolution of compound in ethanol. ¹H NMR (400 MHz DMSO-d6): δ 8.46 (s,1H), 7.70 (s, 1H), 4.37 (s, 1H), 4.09 (m, 4H), 3.81, (m, 4H), 3.45 (q,2H, J=10.1 Hz), 1.61 (s, 6H). ESI MS [MH⁺]: 416.1.

Example 3 Representative Procedure for the Synthesis of Compounds fromSubscaffold 2

To a solution of 2 g of 4-(bromomethyl)phenyl acetic acid in 20 mL ofmethanol was added 0.2 mL of TMSCl and mixture was stirred for 2 hrs.The solvent was removed in vacuo and residue was twice redissolved inMeOH and reconcentrated to give desired product, which was used in thexet step without purification. Bromoester was refluxed in 50 mL of waterin the presence of 2.5 g of sodium bisulfilte for 3 hs. After coolingdown the precipitate was filtered off and dried on the funnel overnight.The solid was suspended in 15 mL of POCl₃ and 1 g of PCl₅ was slowlyadded to a suspension. The mixture stirred for 3 hs at RT. A mixture wasconcentrated and 10 mL of conc. ammonia in water was slowly added to 0°C., redissolved compound in 30 mL of acetonitrile. After stirring for 12hs at RT, a mixture was concentrated, partitioned between ethyl acetateand saturated sodium carbonate solution. Organic layer was washed withbrine, dried over MgSO₄ and evaporated. The intermediate ester wasdissolved in 5 mL of EtOH and 10 ml of 10M NaOH was added. The mixturewas stirred for 24 hs and then concentrated. Acidification with 12M HClresulted in precipitate. 2-(4-(sulfamoylmethyl)phenyl)acetic acid wasfiltered off and dried overnight. Used without purification in the nextstep.

190 mg of 4-chloro-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine (0.75mmol) was added to a stirred solution of 290 mg ofN,N-diisopropylethylamine (2.25 mmol) and 168 mg of 1-Boc-piperazine(0.9 mmol) in 20 mL and was heated at reflux overnight. Solvent wasremoved under reduced pressure and the residue was loaded on silica gelcolumn. Elution with DCM:MeOH produced 215 mg of Boc-intermediate as apale yellow solid. Later it was dissolved in 20 mL of 4M HCl in dioxaneand stirred for 2 hs. Solvent was evaporated under reduced pressure andthe residue was partitioned between ethyl acetate and saturated sodiumcarbonate solution. Organic layer was washed with brine, dried overMgSO₄ and evaporated to afford 150 mg of4-(piperazin-1-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine,which was used in the next step without purification.

23 mg of 2-(4-(sulfamoylmethyl)phenyl)acetic acid (0.1 mmol), 20 mg of4-(piperazin-1-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine(0.067 mmol), 20 mg of EDCI (0.1 mmol) and 4 mg of DMAP (0.033 mmol) wasstirred in 2 mL of DCM. After 2 hs reaction mixture was concentrated andresidue was loaded on silica gel column. Elution with DCM-MeOH 9:1 andevaporation of fraction produced 38 mg of(4-(2-oxo-2-(4-(6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)piperazin-1-yl)ethyl)phenyl)methanesulfonamide(compound 44). ¹H NMR (400 MHz, CDCl₃): δ 8.44 (s, 1H), 7.36 (d, 2H, J=8Hz), 7.25 (d, 2H, J=8 Hz), 7.20 (s, 1H), 4.88 (s, 2H), 4.26 (s, 1H),3.5-4.0 (m, 10H). ESI MS [MH⁺]: 514.1. Its monohydrochloride salt wasobtained by adding 1 equivalent of 1N HCl solution in diethyl ether to asolution of compound in ethanol.

Example 4 Representative Procedure for the Synthesis of Compounds fromSubscaffold 3

4.8 g of 4-chloro-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine (19mmol) was added to a stirred solution of 7.4 g ofN,N-diisopropylethylamine (57 mmol) and 168 mg of 1-Boc-piperazine (0.9mmol) in 95 mL and was heated at reflux overnight. On the morningreaction mixture was evaporated with silica gel and loaded on thecolumn. The product was eluted with hexane-ethyl acetate from 1:1 to 1:5yielding 7.42 g of boc-derivative. Boc-intermediate was dissolved in 40mL of 4M HCl in dioxane and stirred for 2 hs. Solvent was evaporatedunder reduced pressure and the residue was partitioned between ethylacetate and saturated sodium carbonate solution. Organic layer waswashed with brine, dried over MgSO₄ and evaporated to afford 5.3 g ofN-(piperidin-4-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-amine,which was used in later steps without purification. ¹H NMR (600 MHz,CDCl₃): δ 8.47 (s, 1H), 7.13 (s, 1H), 5.32 (d, 1H, J=7.7 Hz), 4.32 (m,1H), 3.64 (q, 2H, 10 Hz), 3.19 (m, 2H), 2.83 (m, 2H), 2.57 (br, 1H),2.14 (m, 2H), 1.55 (m, 2H). ¹³C NMR (150 MHz, CDCl₃): δC 166.85, 155.96,154.33, 128.12, 126.62, 118.66, 116.48, 47.98, 45.32, 35.56 (q, J=31.5Hz), 33.10. ESI MS [MH⁺]: 317.2.

59 mg ofN-(piperidin-4-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-amine(0.19 mmol) and 21 mg of p-hydroxybenzaldehyde (0.19 mmol) weredissolved in 0.5 mL of MeOH in the presence of 10 uL of acetic acid. 19mg of NaBH₃CN (0.3 mmol) was slowly added to that mixture and solutionwas stirred for 24 hs. All volatiles were removed under reduced pressureand residue was partitioned between water and ethyl acetate. Organiclayer was washed with brine, dried over magnesium sulfate andevaporated. The residue was purified on silica gel column withDCM:MeOH:Et3N as eluent resulting in 62 mg of4-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)phenol(compound 105). ¹H NMR (600 MHz, CDCl₃): δ 8.46 (s, 1H), 7.09 (d, 2H,J=8.4 Hz), 7.07 (s, 1H), 6.68 (d, 2H, J=8.4 Hz), 5.28 (d, 1H, J=7.7 Hz),4.21 (m, 1H), 3.59 (q, 2H, 9.9 Hz), 3.46 (s, 2H), 2.96 (m, 2H), 2.21 (m,2H), 2.09 (m, 2H), 1.62 (m, 2H). ¹³C NMR (150 MHz, CDCl₃): δC 166.45,156.08, 155.98, 154.14, 131.01, 128.23, 125.57, 118.65, 116.52, 115.62,62.48, 52.10, 47.96, 35.50 (q, J=31.5 Hz), 31.89. ESI MS [MH⁺]:423.1458. Its monohydrochloride salt was obtained by adding 1 equivalentof 1N HCl solution in diethyl ether to a solution of compound inethanol.

Example 5 Analytical Data for Selected Compounds from Subscaffold 3 and4 and Representative Procedures for their Synthesis Compound 160

Synthesized according to this synthetic route:

Monohydrochloride salt exists as a mixture of rotomers in approximateratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, CD₃OD):δ 8.41 (s, 1H), 7.76 (s, 1H), 7.62 (m, 2H), 7.57 (d, 1H, J=8.3 Hz), 7.33(s, 1H), 4.57 (m, 1H), 4.05 (m, 1H), 3.96 (m, 1H), 3.91 (q, 2H, J=10.3Hz), 3.53 (m, 1H), 3.42 (m, 1H), 3.22 (m, 1H), 2.60 (m, 2H), 2.16 (m,1H), 2.04 (m, 1H). ¹³C NMR (150 MHz, CD₃OD): δC 167.34, 158.35, 154.49,138.61, 130.12, 128.67, 127.53, 127.29, 125.19, 121.45, 118.12, 114.51,113.72, 112.03, 111.14, 53.12, 52.61, 51.47, 51.22, 50.34, 49.41, 35.46(q, J=33 Hz), 30.32. ESI MS [MH⁺]: 486.1676.

Compound 161

Synthesized according to this synthetic route:

Monohydrochloride salt exists as a mixture of rotomers in approximateratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, CD₃OD):δ 9.34 (s, 1H), 8.39 (s, 1H), 7.72 (s, 1H), 7.59 (m, 2H), 7.53 (d, 1H,J=8.3 Hz), 7.29 (s, 1H), 4.51 (m, 1H), 4.02 (m, 1H), 3.91 (m, 1H), 3.88(q, 2H, J=10.3 Hz), 3.54 (m, 2H), 3.51 (m, 1H), 3.41 (m, 2H), 3.19 (m,1H), 2.98 (m, 2H), 2.59 (m, 2H), 2.12 (m, 1H), 2.03 (m, 1H), 1.97 (m,2H), 1.85 (m, 1H), 1.83 (m, 1H). ¹³C NMR (150 MHz, CD₃OD): δC 168.29,164.2, 157.42, 154.41, 139.41, 131.32, 128.62, 127.41, 127.05, 124.49,121.42, 117.12, 113.94, 113.45, 111.97, 111.21, 63.11, 53.31, 52.59,51.42, 51.13, 50.48, 48.31, 48.21, 47.97, 35.48 (q, J=33 Hz), 30.21,28.71, 26.33. ESI MS [MH⁺]: 597.2367.

Compound 162

Synthesized according to this synthetic route:

Monohydrochloride salt exists as a mixture of rotomers in approximateratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, CD₃OD):δ 8.39 (s, 1H), 7.74 (s, 1H), 7.61 (m, 2H), 7.52 (d, 1H, J=8.3 Hz), 7.27(s, 1H), 4.54 (m, 1H), 4.24 (m, 2H), 4.03 (m, 1H), 3.94 (m, 1H), 3.88(q, 2H, J=10.3 Hz), 3.51 (m, 1H), 3.37 (m, 1H), 3.21 (m, 1H), 2.58 (m,2H), 2.16 (m, 1H), 2.03 (m, 1H), 1.28 (m, 1H), 0.59 (m, 2H), 0.48 (m,2H). ¹³C NMR (150 MHz, CD₃OD): δC 167.24, 158.39, 154.62, 138.67,130.19, 128.64, 127.62, 127.38, 125.55, 121.75, 118.37, 114.53, 113.85,112.07, 111.07, 62.75, 53.33, 52.73, 51.39, 51.25, 50.52, 49.43, 35.52(q, J=33 Hz), 31.23, 12.50, 4.18. ESI MS [MH⁺]: 540.2159.

Compound 165

2.4 mL of benzyl bromide (20 mmol) was added dropwise over an hour to asolution of 1.6 mL of pyridine in 5 mL of acetonitrile. Then reactionmixture was heated at 70 to 72° C. for 3 hours. Solvent was removedunder reduced pressure and the residue was dissolved in 16 mL ofethanol. 1.1 g of sodium borohydride (30 mmol) was added in smallportions over 30 minutes. After stirring for 24 hs reaction mixture wascarefully quenched with 50 mL of water and solvents were removed invacuo. The residue was portioned between ethyl acetate and 2M NaOHsolution. Organic extracts were washed with brine, dried over MgSO₄ andevaporated to afford crude 3.36 g of crude1-benzyl-1,2,3,6-tetrahydropyridine which was used in the next stepwithout purification.

3.36 g of 1-benzyl-1,2,3,6-tetrahydropyridine (0.19 mmol) was dissolvedin 35 mL of water containing 1.5 mL of trifluoroacetic acid (0.2 mmol).To that solution 5.87 g of NBS was added in small portions. After 4 hsreaction mixture was transferred to 50 mL of 20% NaOH solution andstirred overnight. On the morning reaction mixture was extracted withdichloromethane and combined organic fractions were dried over sodiumsulfate and concentrated. The residue was purified on silica gel columnusing hexane-ethyl acetate 3:1 as eluent. Evaporation of solventproduced 1.2 g of 3-benzyl-7-oxa-3-azabicyclo[4.1.0]heptane as colorlessoil.

A solution of 1.2 g of 3-benzyl-7-oxa-3-azabicyclo[4.1.0]heptane (6.3mmol) was refluxed in the presence of 0.62 g of sodium azide (9.5 mmol)and 3 g of lithium perchlorate (19 mmol) for 4 hs. After completionreaction mixture was evaporated and the residue was extracted withdichloromethane, washed with water and combined organic fractions weredried over sodium sulfate and concentrated. The residue was purified onsilica gel column using hexane-ethyl acetate 4:1 as eluent affording 980mg of trans-4-azido-1-benzylpiperidin-3-ol.

201 mg of trans-4-azido-1-benzylpiperidin-3-ol (0.87 mmol) was dissolvedin 3 ml of EtOH-water 3:1. To that solution 77 mg of zinc (12 mmol), 112mg of ammonium chloride (2.1 mmol) were added and heterogeneous mixturewas refluxed for 10 minutes. After cooling down reaction mixture wasdiluted with 8 mL of ethyl acetate and 0.5 mL of conc. ammonia in water,filtered off. Organic layer washed with brine, dried over sodium sulfateand evaporated. The residue was purified on silica gel column usingDCM:MeOH 10:1 as eluent affording 120 mg oftrans-4-amino-1-benzylpiperidin-3-ol.

The mixture of 36.7 mg of trans-4-amino-1-benzylpiperidin-3-ol (0.18mmol), 30 mg of 4-chloro-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine(0.12 mmol) and 46 mg of N,N-diisopropylethylamine (0.36 mmol) wasrefluxed in 0.75 mL of isopropanol for 18 hs. Then reaction mixture wasconcentrated and purified on silica gel column eluting with DCM:MeOH20:1 to afford 45 mf oftrans-1-benzyl-4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-3-ol(Compound 165). Its monohydrochloride salt was obtained by adding 1equivalent of 1N HCl solution in diethyl ether to a solution of compoundin ethanol. ¹H NMR (600 MHz, CD₃OD) of HCl salt, signals are allbroadened because of intramolecular H-bond: δ 8.37 (1H), 7.51-7.60 (6H),4.43 (4H), 4.12 (1H), 3.85 (2H), 3.55 (2H), 3.21 (1H), 2.99 (1H), 2.06(1H). ¹³C NMR (150 MHz, CD₃OD): δC 165.78, 158.45, 153.97, 132.59,131.46, 130.51, 130.18, 127.45, 125.62, 122.09, 118.50, 68.02, 61.86,56.88, 54.15, 52.38, 35.81 (q, J=31.5 Hz), 28.14. ESI MS [MH⁺]:423.1458.

Compound 167

Monohydrochloride salt exists as a mixture of rotomers in approximateratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, CD₃OD):δ 8.69 (s, 1H), 7.87 (s, 1H), 7.66 (m, 2H), 7.55 (m, 3H), 7.44 (m, 2H) m7.34 (m, 2H), 5.13 (m, 1H), 4.53 (m, 3H), 4.35 (m, 2H), 4.07 (m, 1H),3.99 (q, 2H, J=10.3 Hz), 3.75 (m, 1H), 3.63 (m, 1H), 3.42 (m, 1H), 2.41(m, 2H). ¹³C NMR (150 MHz, CD₃OD): δC 159.23, 158.93, 151.86, 132.75,132.67, 132.65, 131.70, 130.59, 129.75, 129.20, 127.37, 125.54, 122.78,119.37, 4095, 38.63, 35.33 (q, J=33 Hz), 33.39, 33.25, 33.15, 25.98,25.97. ESI MS [MH⁺]: 512.2095.

Example 6 Analytical Data for Selected Compounds from Subscaffold 4 andRepresentative Procedures for Their Synthesis Compound 175

A mixture of 0.5 g of 5-methylindole-2-carboxylic acid, 0.25 mL ofthionyl chloride, 5 mL of chloroform and small drop of DMF was refluxedfor 2 hs. The reaction mixture was cooled to RT, poured into a mixtureof 5 g of ice and 5 mL of 25% ammonia solution, and then stirred for 2hs. The precipitated product was filtered off, washed with water anddried to yield 350 mg of 5-methylindole-2-carboxamide. ¹H NMR (600 MHz,DMSO-d6): δ 11.37 (s, 1H), 7.89 (br, 1H), 7.36 (s, 1H), 7.30 (d, 1H,J=8.4 Hz), 7.28 (br, 1H), 7.02 (s, 1H), 6.99, (d, 1H, J=8.4 Hz), 2.36(s, 3H). ¹³C NMR (150 MHz, CDCl₃): δC 160.95, 132.95, 129.77, 126.15,125.44, 123.10, 118.77, 110.02, 100.65, 19.20.

A mixture of 340 mg of 5-methylindole-2-carboxamide (1.95 mmol), 1.5 gof phosphorus oxychloride (9.75) and 8 mL of chloroform was refluxed for2 hs. Then cooled solution was poured into 20 mL of water and stirredfor 1 hr. After separation the organic layer was dried over sodiumsulfate and concentrated. The residue was purified on silica gel columnusing hexane-ethyl acetate 5:1 to afford 245 mg of5-methyl-1H-indole-2-carbonitrile. ¹H NMR (600 MHz, CDCl₃): δ 8.61 (br,1H), 7.44 (s, 1H), 7.30 (d, 1H, J=8.4 Hz), 7.21 (d, 1H, J=8.4 Hz), 7.11(s, 1H), 2.44 (s, 3H). ¹³C NMR (150 MHz, CDCl₃): δC 135.34, 131.25,128.28, 126.53, 121.33, 114.41, 113.95, 111.39, 106.11, 21.36.

To a solution of 245 mg of 5-methyl-1H-indole-2-carbonitrile (1.6 mmol)in 5 mL of acetonitrile 0.434 mL of di-tert-butyl dicarbonate (1.9 mmol)and 29 mg of DMAP (0.24 mmol) were added and stirred at room temperaturefor 30 min. The solvent was removed in vacuo, and the resultant crudeproduct was purified by column chromatography (silica gel) using purehexane-ethyl acetate 10:1 as an eluant to afford 334 mg of tert-butyl2-cyano-5-methyl-1H-indole-1-carboxylate. ¹H NMR (600 MHz, CDCl3): δ8.10 (d, 1H, J=8.8 Hz), 7.39 (s, 1H), 7.31 (d, 1H, J=8.8 Hz), 7.26 (s,1H), 2.45 (s, 3H), 1.72, (s, 9H). ¹³C NMR (150 MHz, CDCl₃): δC 148.22,134.94, 133.78, 129.85, 121.61, 121.24, 115.53, 113.46, 108.76, 85.54,28.05, 21.21.

To a stirred solution of 334 mg of tert-butyl2-cyano-5-methyl-1H-indole-1-carboxylate (1.3 mmol) in carbontetrachloride (5 mL) was added 232 mg of N-bromosuccinimide (1.3 mmol)and 11 mg of AIBN (0.065 mmol). The mixture was refluxed for 1 h, thencooled and concentrated, and the residues were purified bychromatography on silica gel using hexane-ethyl acetate 20:1 to give 340mg of tert-butyl 2-cyano-5-bromomethyl-1H-1-indole-1-carboxylate. ¹H NMR(600 MHz, CDCl3): δ 8.22 (d, 1H, J=8.8 Hz), 7.64 (s, 1H), 7.53 (d, 1H,J=8.8 Hz), 7.31 (s, 1H), 4.60 (s, 2H), 1.73, (s, 9H). ¹³C NMR (150 MHz,CDCl₃): δC 147.64, 136.27, 133.92, 129.34, 127.45, 122.33, 121.15,116.46, 113.02, 109.75, 87.14, 33.23, 28.01.

16.7 mg of tert-butyl 2-cyano-5-bromomethyl-1H-1-indole-1-carboxylate(0.05 mmol) and 15.8 mg ofN-(piperidin-4-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-amine(0.05 mmol) were dissolved in 0.6 mL of DCM. 12.9 mg of DIPEA (0.1 mmol)was added to that solution and reaction mixture was stirred for 18 hs.Then reaction mixture was directly loaded on silica gel column and theproduct was eluted with DCM-MeOH 30:1. After evaporation of solventboc-protected intermediate was dissolved in 0.5 mL of ACN and 0.06 mL ofSnCl₄ (0.5 mmol) was added. The homogenous reaction mixture was stirredfor 1 h and then all volatiles were removed in vacuo. The residue wasquenched ammonia and extracted with ethyl acetate. Combined organicfractions were dried over MgSO₄ and concentrated. The residue waspurified on silica gel column using hexane-ethyl acetate-MeOH 1:1:0.1 toproduce 16 mg of5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile(Compound 175). Its monohydrochloride salt was obtained by adding 1equivalent of 1N HCl solution in diethyl ether to a solution of compoundin ethanol. The hydrochloride salt was recrystallized from methanol. ¹HNMR (600 MHz, DMSO-d6): δ 12.62 (s, 1H), 10.74 (br, 1H), 8.33 (s, 1H),8.07 (d, 1H, J=7 Hz), 7.93, s, 1H), 7.70 (s, 1H), 7.62 (d, 1H, J=12 Hz),7.56 (d, 1H, J=12 Hz), 7.45 (s, 1H), 4.36 (s, 1H), 4.30 (m, 1H), 4.03(q, 2H, J=11 Hz), 3.41 (m, 2H), 3.11 (m, 2H), 2.12 (m, 2H), 1.98 (m,2H). ¹³C NMR (150 MHz, DMSO-d6): δC 165.88, 155.72, 153.78, 137.18,128.42, 126.97, 125.78, 125.37, 124.52, 122.22, 121.31, 116.12, 114.22,113.36, 112.54, 106.84, 59.27, 50.36, 45.46, 33.73 (q, J=33 Hz), 28.23.ESI MS [MH⁺]: 471.1579.

Compound 177

Monohydrochloride salt exists as a mixture of rotomers in approximateratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz,MeOD-d4): 8.68 (s, 1H), 7.94 (s, 1H), 7.82 (s, 1H), 7.69 (d, 1H, J=8.4Hz), 7.62 (d, 1H, J=8.4 Hz), 7.35 (s, 1H), 4.63 (m, 1H), 4.48 (s, 2H),4.45 (q, 2H, J=7.2 Hz), 3.99 (q, 2H, J=10.3 Hz), 3.63 (m, 2H), 3.26 (m,2H), 2.34 (m, 2H), 2.14 (m, 2H), 1.45 (t, 3H, 7.2 Hz). ¹³C NMR (150 MHz,MeOD-d4): δC 149.93, 138.83, 132.93, 129.40, 127.94, 127.30, 127.26,125.43, 123.06, 122.70, 118.69, 114.30, 113.86, 112.75, 112.60, 111.75,62.02, 52.39, 48.39, 41.53, 35.22 (q, J=33 Hz), 29.53, 15.76. ESI MS[MH⁺]: 499.1891.

Compound 178

Monohydrochloride salt exists as a mixture of rotomers in approximateratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz,MeOD-d4): 8.40 (s, 1H), 7.94 (s, 1H), 7.72 (d, 1H, J=8.8 Hz), 7.61 (d,1H, J=8.8 Hz), 7.59 (s, 1H), 7.35 (s, 1H), 4.48 (m, 3H), 4.27 (m, 2H),4.88 (q, 2H, J=10.6 Hz), 3.61 (m, 2H), 3.25 (m, 2H), 2.34 (m, 2H), 2.02(m, 2H), 1.30 (m, 1H), 0.58 (m, 2H), 0.50 (m, 2H). ¹³C NMR (150 MHz,MeOD-d4): δC 164.91, 157.63, 153.86, 139.38, 130.60, 129.39, 127.91,127.49, 127.17, 125.66, 123.22, 121.97, 118.29, 114.36, 112.89, 112.18,61.96, 52.69, 50.85, 47.34, 35.54 (q, J=33 Hz), 29.95, 12.65, 4.38. ESIMS [MH⁺]: 525.2052.

Compound 179

Monohydrochloride salt exists as a mixture of rotomers in approximateratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz,MeOD-d4): 8.75 (s, 1H), 7.96 (s, 1H), 7.88 (d, 1H, J=8.8 Hz), 7.74 (d,1H, J=8.8 Hz), 7.64 (s, 1H), 7.37 (s, 1H), 4.67 (m, 1H), 4.51 (m, 3H),4.03 (q, 2H, J=10.6 Hz), 3.93 (m, 2H), 3.65 (m, 2H), 3.30 (m, 2H), 2.36(m, 2H), 2.18 (m, 2H). ¹³C NMR (150 MHz, MeOD-d4): δC 164.91, 139.70,133.26, 129.21, 127.95, 127.11, 127.10, 125.48, 123.11, 122.84, 122.79,118.74, 114.21, 113.09, 112.99, 61.95, 61.79, 52.29, 49.60, 48.54, 35.12(q, J=33 Hz), 29.45. ESI MS [MH⁺]: 515.1828.

Compound 180

To the mixture of 2.46 g of 2-methoxy-3-methylanisaldehyde (16 mmol) and4.72 g of methyl azidoacetate (41 mmol) in 20 mL of MeOH is added 7.6 mLof 5.4M MeONa over 30 minute at −10 degrees. After addition the mixturewas stirred for additional hour at the same temperature and thentransferred in cold room (4 degrees) and stirred overnight. On themorning reaction mixture was poured in 0.5 L mixture of ice and conc.ammonium chloride solution, stirred for 10 minutes and filtered off. Thesolid was washed with plenty of ice cold water and then moved at ambienttemperature. After air drying for 1 hr the solid was dissolved in 50 mLof DCM, dried over magnesium sulfate and passed through short silica gelplug. Evaporation of solvent produced 3.5 g of methyl2-azido-3-(2-methoxy-3-methylphenyl)acrylate, that was used in the nextstep without further purification.

4.16 g of methyl 2-azido-3-(2-methoxy-3-methylphenyl)acrylate (16.8mmol) was dissolved in 20 mL of toluene. 560 mg of rhodium (II)trifluoroacetate dimer (0.84 mmol) was added and the reaction mixturewas heated at 50 degrees for 24 hs. Then solvent was evaporated andresidue was loaded on silica gel column and eluted with hexane-ethylacetate 10:1 to produce after evaporation 1.3 g of methyl4-methoxy-5-methyl-1H-indole-2-carboxylate. ¹H NMR (600 MHz, CDCl₃): δ9.05 (br, 1H), 7.32 (s, 1H), 7.11 (d, 1H, J=8 Hz), 7.04 (d, 1H, J=8 Hz),4.03 (s, 3H), 3.94 (s, 1H), 2.33 (s, 1H).

80 mg of methyl 4-methoxy-5-methyl-1H-indole-2-carboxylate (0.39 mmol)was heated at 80 degrees in a sealed tube with 1 mL of 7M ammonia inmethanol. After one week reaction the solvent evaporated to produce 79mg of 4-methoxy-5-methyl-1H-indole-2-carboxamide that was used withoutpurification in the next step.

A mixture of 79 mg of 4-methoxy-5-methyl-1H-indole-2-carboxamide (0.39mmol), 0.19 mL of phosphorus oxychloride (2 mmol) and 1.5 mL ofchloroform was refluxed for 2 hs. Then cooled solution was poured into10 mL of water and stirred for 1 hr. After separation the organic layerwas dried over sodium sulfate and concentrated. The residue was purifiedon silica gel column using hexane-ethyl acetate 5:1 to afford 51 mg of4-methoxy-5-methyl-1H-indole-2-carbonitrile.

To a solution of 390 mg of 4-methoxy-5-methyl-1H-indole-2-carbonitrile(2.1 mmol) in 7 mL of acetonitrile 0.574 mL of di-tert-butyl bicarbonate(0.74 mmol) and 25 mg of DMAP (0.21 mmol) were added and stirred at roomtemperature for 30 min. The solvent was removed in vacuo, and theresultant crude product was purified by column chromatography (silicagel) using hexane-ethyl acetate 10:1 as an eluent to afford 561 mg oftert-butyl 2-cyano-4-methoxy-5-methyl-1H-indole-1-carboxylate.

To a stirred solution of 561 mg of tert-butyl2-cyano-4-methoxy-5-methyl-1H-indole-1-carboxylate (1.96 mmol) in carbontetrachloride (9 mL) was added 349 mg of N-bromosuccinimide (1.96 mmol)and 64 mg of AIBN (0.39 mmol). The mixture was refluxed for 1 h, thencooled and concentrated and filtered through short silica gel plug usinghexane-ethyl acetate 10:1 to give 852 mg of crude tert-butyl5-(bromomethyl)-2-cyano-4-methoxy-1H-indole-1-carboxylate that was usedin the next step without further purification.

852 mg of crude tert-butyl 2-cyano-5-bromomethyl-1H-indole-1-carboxylate(1.96 mmol) and 829 mg ofN-(piperidin-4-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-amine(2.62 mmol) were dissolved in 5 mL of DCM. 1.3 mL of DIPEA (7.5 mmol)was added to that solution and reaction mixture was stirred for 18 hs.Then reaction mixture was directly loaded on silica gel column and theproduct was eluted with Hexane-Ethyl acetate-MeOH 2:1:0.1. Afterevaporation of solvent boc-protected intermediate was dissolved in 14 mLof ACN and 1.7 mL of SnCl₄ (0.5 mmol) was added. The homogenous reactionmixture was stirred for 1 h and then all volatiles were removed invacuo. The residue was quenched ammonia and extracted with ethylacetate. Combined organic fractions were dried over MgSO₄ andconcentrated. The residue was purified on silica gel column usinghexane-ethyl acetate-MeOH 1:1:0.2 to produce 494 mg of4-methoxy-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile(Compound 180). Its monohydrochloride salt was obtained by adding 1equivalent of 1N HCl solution in diethyl ether to a solution of compoundin ethanol. Monohydrochloride salt exists as a mixture of rotomers inapproximate ratio 10:1, NMR is described for the major one: ¹H NMR (600MHz, MeOD-d4): δ 8.71 (s, 1H), 7.85 (s, 1H), 7.60 (s, 1H), 7.45 (d, 1H,J=8 Hz), 7.23 (d, 1H, J=8 Hz), 4.63 (m, 1H), 4.46 (s, 2H), 4.29 (s, 3H),4.01 (q, 2H, J=10.5 Hz), 3.64 (m, 2H), 3.29 (m, 2H), 2.33 (m, 2H), 2.13(m, 2H). ¹³C NMR (150 MHz, MeOD-d4): δC 155.08, 149.56, 142.48, 133.14,130.79, 130.44, 127.31, 123.36, 122.79, 118.72, 118.60, 114.63, 113.09,110.78, 107.95, 108.25, 61.21, 56.92, 52.45, 35.11 (q, J=33 Hz), 29.50.ESI MS [MH⁺]: 501.1684.

Compounds 181 and 182

To the mixture of 6.59 g of 3-methylanisaldehyde (44 mmol) and 12.65 gof methyl azidoacetate (110 mmol) in 60 mL of MeOH is added 20 mL of5.4M MeONa over 30 minute at −10 degrees. After addition the mixture wasstirred for additional hour at the same temperature and then transferredin cold room (4 degrees) and stirred overnight. On the morning reactionmixture was poured in 1 L mixture of ice and conc. ammonium chloridesolution, stirred for 10 minutes and filtered off. The solid was washedwith plenty of ice cold water and then moved at ambient temperature.After air drying for 1 hr the solid was dissolved in 50 mL of DCM, driedover magnesium sulfate and passed through short silica gel plug.Evaporation of solvent produced 9.8 g of methyl2-azido-3-(4-methoxy-3-methylphenyl)acrylate, that was used in the nextstep without further purification.

250 mg of 2-azido-3-(4-methoxy-3-methylphenyl)acrylate (1 mmol) wasdissolved in 1 mL of toluene. 30 mg of rhodium (II) trifluoroacetatedimer (0.045 mmol) was added and the reaction mixture was heated at 50degrees for 24 hs. Then solvent was evaporated and residue was loaded onsilica gel column and eluted with hexane-ethyl acetate 10:1 to produceafter evaporation 125 mg of methyl6-methoxy-5-methyl-1H-indole-2-carboxylate. ¹H NMR (600 MHz, CDCl₃): δ8.73 (br, 1H), 7.39 (s, 1H), 7.10 (s, 1H), 6.77 (s, 1H), 3.92 (s, 3H),3.88 (s, 1H), 2.28 (s, 1H).

200 mg of methyl 6-methoxy-5-methyl-1H-indole-2-carboxylate (1 mmol) washeated at 80 degrees in a sealed tube with 2 mL of 7M ammonia inmethanol. After one week reaction the solvent evaporated to produce 202mg of 6-methoxy-5-methyl-1H-indole-2-carboxamide that was used withoutpurification in the next step.

A mixture of 202 mg of 6-methoxy-5-methyl-1H-indole-2-carboxamide (1mmol), 0.47 mL of phosphorus oxychloride (5 mmol) and 3 mL of chloroformwas refluxed for 2 hs. Then cooled solution was poured into 10 mL ofwater and stirred for 1 hr. After separation the organic layer was driedover sodium sulfate and concentrated. The residue was purified on silicagel column using hexane-ethyl acetate 5:1 to afford 116 mg of6-methoxy-5-methyl-1H-indole-2-carbonitrile. ¹H NMR (600 MHz, CDCl₃): δ8.26 (br, 1H), 7.37 (s, 1H), 7.06 (s, 1H), 6.76 (s, 1H), 3.88 (s, 1H),2.28 (s, 3H).

To a solution of 116 mg of 6-methoxy-5-methyl-1H-indole-2-carbonitrile(0.62 mmol) in 2 mL of acetonitrile 0.171 mL of di-tert-butylbicarbonate (0.74 mmol) and 20 mg of DMAP (0.24 mmol) were added andstirred at room temperature for 30 min. The solvent was removed invacuo, and the resultant crude product was purified by columnchromatography (silica gel) using hexane-ethyl acetate 10:1 as an eluentto afford 174 mg of tert-butyl2-cyano-6-methoxy-5-methyl-1H-indole-1-carboxylate.

To a stirred solution of 174 mg of tert-butyl2-cyano-6-methoxy-5-methyl-1H-indole-1-carboxylate (0.61 mmol) in carbontetrachloride (2.5 mL) was added 108 mg of N-bromosuccinimide (0.61mmol) and 11 mg of AIBN (0.065 mmol). The mixture was refluxed for 1 h,then cooled and concentrated and filtered through short silica gel plugusing hexane-ethyl acetate 10:1 to give 223 mg of crude tert-butyl5-(bromomethyl)-2-cyano-6-methoxy-1H-indole-1-carboxylate that was usedin the next step without further purification.

223 mg of tert-butyl 2-cyano-5-bromomethyl-1H-indole-1-carboxylate (0.61mmol) and 193 mg ofN-(piperidin-4-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-amine(0.61 mmol) were dissolved in 2 mL of DCM. 0.22 mL of DIPEA (0.2 mmol)was added to that solution and reaction mixture was stirred for 18 hs.Then reaction mixture was directly loaded on silica gel column and theproduct was eluted with DCM-MeOH 30:1. After evaporation of solventboc-protected intermediate was dissolved in 0.5 mL of ACN and 0.06 mL ofSnCl₄ (0.5 mmol) was added. The homogenous reaction mixture was stirredfor 1 h and then all volatiles were removed in vacuo. The residue wasquenched ammonia and extracted with ethyl acetate. Combined organicfractions were dried over MgSO₄ and concentrated. The residue waspurified on silica gel column using hexane-ethyl acetate-MeOH 1:1:0.1 toproduce 210 mg of6-methoxy-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile(Compound 181). Its monohydrochloride salt was obtained by adding 1equivalent of 1N HCl solution in diethyl ether to a solution of compoundin ethanol. Monohydrochloride salt exists as a mixture of rotomers inapproximate ratio 10:1, NMR is described for the major one: ¹H NMR (600MHz, MeOD-d4): δ 8.71 (s, 1H), 7.87 (s, 1H), 7.86 (s, 1H), 7.24 (s, 1H),7.12 (s, 1H), 4.66 (m, 1H), 4.49 (s, 2H), 4.03 (m, 5H), 3.69 (m, 2H),3.34 (m, 2H), 2.36 (m, 2H), 2.18 (m, 2H). ¹³C NMR (150 MHz, MeOD-d4): δC158.72, 149.70, 140.86, 133.08, 128.17, 127.75, 127.31, 12,3.36, 122.81,121.69, 118.72, 115.07, 114.82, 114.60, 107.47, 94.60, 57.67, 56.62,52.72, 35.22 (q, J=33 Hz), 29.53. ESI MS [MH⁺]: 501.1675.

500 mg of6-methoxy-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile(1 mmol) was slowly added to 5 mL of 1M BBr₃ in DCM at 0 degrees andreaction mixture was brought to RT. After 4 days ice was added toreaction mixture in the presence of sodium bicarbonate. Volatile organicwas evaporated and the residue was partitioned between water and ethylacetate-methanol 10:1. Organic layer was evaporated with silica gel andloaded on the column. The product was eluted with hexane-ethylacetate-methanol 1:1:0.1, evaporation of fractions produced 300 mg of6-hydroxy-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile(Compound 182). Its monohydrochloride salt was obtained by adding 1equivalent of 1N HCl solution in diethyl ether to a solution of compoundin ethanol. Monohydrochloride salt exists as a mixture of rotomers inapproximate ratio 10:1, NMR is described for the major one: ¹H NMR (600MHz, MeOD-d4): 8.70 (s, 1H), 7.81 (s, 1H), 7.77 (s, 1H), 7.21 (s, 1H),6.98 (s, 1H), 4.64 (m, 1H), 4.48 (s, 1H), 4.01 (q, 2H, J=10.3 Hz), 3.66(m, 2H), 3.35 (m, 2H), 2.37 (m, 2H), 2.12 (m, 2H). ¹³C NMR (150 MHz,MeOD-d4): δC 157.64, 156.62, 153.92, 141.09, 130.54, 127.75, 127.48,125.65, 121.96, 121.59, 118.27, 115.23, 114.85, 113.98, 107.11, 97.45,57.78, 52.88, 47.29, 35.54 (q, J=33 Hz), 29.95. ESI MS [MH⁺]: 487.1519.

Compound 186

Monohydrochloride salt exists as a mixture of rotomers in approximateratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz,MeOD-d4): 8.37 (s, 1H), 8.08 (s, 1H), 7.74 (d, 1H, J=8.8 Hz), 7.69 (s,1H), 7.64 (d, 1H, J=8.8 Hz), 7.54 (s, 1H), 4.74 (m, 1H), 4.48 (m, 3H),3.88 (q, 2H, J=10.6 Hz), 3.60 (m, 2H), 3.21 (m, 2H), 2.34 (m, 2H), 2.05(m, 2H). ESI MS [MH⁺]: 514.1998.

Compound 188

331 mg of (R)-3-chloropropane-1,2-diol (3 mmol) and 530 mg of imidazole(7.8 mmol) were dissolved in 5 mL of dry dichloromethane. Then 7.2 mL of1M TBDMSCl in dichloromethane was added. Reaction mixture was stirredovernight and then diluted with 20 mL of water. After separation theorganic layer was dried over sodium sulfate and concentrated to produce850 mg of(R)-5-(chloromethyl)-2,2,3,3,8,8,9,9-octamethyl-4,7-dioxa-3,8-disiladecane.The material was used as is in the next step.

To a solution of 39 mg of 5-methyl-1H-indole-2-carbonitrile (0.25 mmol)in 0.5 mL of DMF 15 mg of NaH (60% in oil, 0.375 mmol) was added andmixture was stirred for 30 min. Then 170 mg of(R)-5-(chloromethyl)-2,2,3,3,8,8,9,9-octamethyl-4,7-dioxa-3,8-disiladecane(0.5 mmol) was added and stirring continued for 24 hs. The reactionmixture was diluted with 10 mL of water and extracted with DCM. Combinedorganic extracts dried over sodium sulfate, concentrated and purifiedusing silica gel column eluting with hexane-ethyl acetate 50:1 to afford56 mg of(S)-1-(2,3-bis((tert-butyldimethylsilyl)oxy)propyl)-5-methyl-1H-indole-2-carbonitrile.¹H NMR (600 MHz, CDCl₃): δ 8.09 (d, 1H, J=8.8 Hz), 7.35 (s, 1H), 7.24(d, 1H, J=8.8 Hz), 7.18 (s, 1H), 4.04 (m, 1H), 3.82 (m, 1H), 3.77 (m,2H), 3.68 (m, 1H), 2.43 (s, 3H), 1.08 (m, 18H), 0.26 (m, 12H).

To a stirred solution of 55 mg of(S)-1-(2,3-bis((tert-butyldimethylsilyl)oxy)propyl)-5-methyl-1H-indole-2-carbonitrile(0.12 mmol) in carbon tetrachloride (0.5 mL) was added 21.3 mg ofN-bromosuccinimide (0.12 mmol) and 1.1 mg of AIBN (0.0065 mmol). Themixture was refluxed for 1 h, then cooled, concentrated and filteredthrough short silica gel plug using hexane-ethyl acetate 10:1 to give 58mg of crude(S)-1-(2,3-bis((tert-butyldimethylsilyl)oxy)propyl)-5-(bromomethyl)-1H-indole-2-carbonitrilethat was used in the next step without further purification.

58 mg of(S)-1-(2,3-bis((tert-butyldimethylsilyl)oxy)propyl)-5-(bromomethyl)-1H-indole-2-carbonitrile(0.1 mmol) and 31 mg ofN-(piperidin-4-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-amine(0.12 mmol) were dissolved in 0.2 mL of DCM. 26 mg of DIPEA (0.2 mmol)was added to that solution and reaction mixture was stirred for 18 hs.Then reaction mixture was directly loaded on silica gel column and theproduct was eluted with DCM-MeOH 30:1. After evaporation of solventTBDMS-protected intermediate was dissolved in 0.2 mL of MeOH and 0.02 mLof 12M HCl was added. The homogenous reaction mixture was stirredovernight and then all volatiles were removed in vacuo. The residue wasquenched ammonia and extracted with ethyl acetate. Combined organicfractions were dried over MgSO₄ and concentrated. The residue waspurified on silica gel column using DCM-MeOH 20:1 to afford 15.9 mg of5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile(Compound 188). Its monohydrochloride salt was obtained by adding 1equivalent of 1N HCl solution in diethyl ether to a solution of compoundin ethanol. Monohydrochloride salt exists as a mixture of rotomers inapproximate ratio 10:1, NMR is described for the major one: ¹H NMR (600MHz, MeOD-d4): 8.63 (s, 1H), 7.95 (s, 1H), 7.78 (s, 1H), 7.77 (d, 1H,J=8.6 Hz), 7.63 (d, 1H, J=8.6 Hz), 7.37 (s, 1H), 4.57 (m, 1H), 4.56 (m,1H), 4.50 (s, 2H) 4.37 (m, 1H), 4.04 (m, 1H), 3.99 (q, 2H, J=10.3 Hz),3.65 (m, 2H), 3.60 (d, 2H, J=5.5 Hz), 3.29 (m, 2H), 2.37 (m, 2H), 2.12(m, 2H). ¹³C NMR (150 MHz, MeOD-d4): δC 157.45, 150.99, 139.90, 132.27,129.16127.89, 127.37, 127.00, 125.54, 123.11, 122.50, 118.58, 114.32,114.25, 113.35, 113.31, 72.35, 64.85, 61.99, 52.44, 49.82, 48.12, 35.32(q, J=33 Hz), 29.64. ESI MS [MH⁺]: 545.1941.

Compound 189

760 mg of5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrilehydrochloride (1.5 mmol) and 207 mg of bromoacetamide (1.5 mmol) weredissolved in 3.6 mL of dry DMF. 1.96 g of cesium carbonate (6 mmol) wasadded and reaction mixture was stirred for 4 hs. Then it was quenchedwith 50 mL of water and extracted with DCM-MeOH 10:1. Combined organicextracts were evaporated with silica gel and loaded on column. Theproduct was eluted with DCM-MeOH 10:1 mixture. After evaporation ofproduct containing fractions it was recrystallized from MeOH to produce319 mg of2-(2-cyano-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indol-1-yl)acetamide,which was converted to hydrochloride salt by dissolving in 5 mL of MeOH,adding of 1 eq of 1M HCl in water. Hydrochloride salt can berecrystallized further from MeOH. Monohydrochloride salt exists as amixture of rotomers in approximate ratio 10:1, NMR is described for themajor one: ¹H NMR (600 MHz, MeOD-d4): 8.44 (s, 1H), 7.91 (s, 1H), 7.57(m, 2H), 7.41 (s, 1H), 5.10 (s, 2H), 4.53 (m, 1H), 4.47 (s, 1H), 3.89(q, 2H, J=10.3 Hz), 3.62 (m, 2H), 3.24 (m, 2H), 2.35 (m, 2H), 1.93 (m,2H). ¹³C NMR (150 MHz, MeOD-d4): δC 171.07, 157.66, 153.62, 140.17,130.77, 129.55, 127.95, 127.10, 125.64, 123.46, 121.90, 118.31, 114.76,113.69, 113.52, 112.60, 61.96, 52.67, 49.60, 47.98, 47.40, 35.52 (q,J=33 Hz), 29.96. ESI MS [MH⁺]: 528.1783.

Compound 206

Monohydrochloride salt exists as a mixture of rotomers in approximateratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz,MeOD-d4): 8.56 (s, 1H), 7.94 (d, 1H, J=8.4 Hz), 7.89 (m, 2H), 7.70, (s,1H), 7.46 (d, 1H, J=8.4 Hz), 4.60 (s, 2H), 4.54 (m, 1H), 3.93 (q, 2H,J=10.6 Hz), 3.67 (m, 2H), 3.28 (m, 2H), 2.35 (m, 2H), 2.04 (m, 2H). ¹³CNMR (150 MHz, MeOD-d4): δC 157.52, 151.57, 136.80, 134.03, 131.92,127.24, 125.41, 124.16, 124.12, 122.23, 121.02, 120.49, 118.48, 118.12,105.91, 104.66, 52.19, 52.06, 47.81, 35.43 (q, J=33 Hz), 29.73. ESI MS[MH⁺]: 471.1576.

Example 7 Representative Procedure for the Synthesis of Compounds fromSubscaffold 5

Tert-butyl4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-ylamino)methyl)piperidine-1-carboxylate.To a solution of4-chloro-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine (50 mg, 0.20mmol) in DMF (1 mL) was added N,N-diisopropylethylamine (52 μL, 0.30mmol) and tert-butyl 4-(aminomethyl)piperidine-1-carboxylate (51 mg,0.30 mmol). The solution was heated to 80° C. for 2 hours. The solutionwas diluted with EtOAc (10 mL) and washed with 10% NaHCO₃ (2×5 mL). Theorganic phase was dried Na₂SO₄ and evaporated in vacuo to give theproduct as a clear oil (103 mg, 80% yield) which was used withoutfurther purification. LC-MS: 2.49 min, 431.2 m/z [M+H]⁺, 375.1 m/z[M-t-Bu+H]⁺

6-(2,2,2-trifluoroethyl)-N-((piperidin-4-yl)methyl)thieno[2,3-d]pyrimidin-4-amine.Tert-butyl4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-ylamino)methyl)piperidine-1-carboxylate(103 mg, 0.24 mmol) was dissolved in TFA (1 mL). The solution wasmaintained at room temperature for 2 hours. The solution was thendiluted with CHCl₃ (10 mL), and washed with 10% NaHCO₃ (2×5 mL). Theorganic phase was dried over Na₂SO₄ and evaporated in vacuo to give theproduct as a clear oil (56 mg, 85% yield). LC-MS: 1.48 min, 331.2 m/z[M+H]⁺.

To a vial containing6-(2,2,2-trifluoroethyl)-N-((piperidin-4-yl)methyl)thieno[2,3-d]pyrimidin-4-amine(20 mg, 0.061 mmol) was added 1,2-dichloroethane (300 uL),3-chloro-4-formylbenzene-1-sulfonamide (17 mg, 0.077 mmol), and sodiumtri(acetoxy)borohydride (20 mg, 0.094 mmol). The mixture was stirred atroom temperature for 4 hours. The mixture was diluted with EtOAc (5 mL),and washed with 0.1 N NaOH (2×1 mL). The volatiles were removed invacuo. The resulting residue was purified by reversed-phase preparativeHPLC (95:5-5:95 MeCN/H₂O with 0.1% TFA buffer). The product containingfractions were evaporated in vacuo to afford the product as a whitesolid (2.7 mg, 8.4% yield), Compound 253. LC-MS: 1.20 min, 534.1 m/z[M+H]⁺

Example 8 Representative Procedure for the Synthesis of Compounds fromSubscaffold 3 and 4

5-(ethoxycarbonyl)-2-(2,2,2-trifluoroethyl)thieno[2,3-b]pyridin-4-yltrifluoromethanesulfonate. Ethyl2-(2,2,2-trifluoroethyl)-4,5-dihydro-4-oxothieno[2,3-b]pyridine-5-carboxylate(91 mg, 0.30 mmol) (synthesized using similar procedure described inliterature procedure J. Het. Chem. 1991, 28(8), 1953-5) was dissolved indichloromethane (5 mL). N,N-diisopropylethylamine (157 uL, 0.90 mmol)was added. Solid N-phenyl-bis(trifluoromethanesulfonamide) (214 mg, 0.60mmol) was added, and the mixture stirred for 10 minutes. The solutionwas washed with water (5 mL), dried over Na₂SO₄, and concentrated invacuo to give an orange residue. Purification of the residue by silicagel chromatography (98:2 hexanes/EtOAc) afforded the product as a yellowsolid (108 mg, 82% yield). LC-MS 3.22 min 438.2 m/z [M+H]⁺

Ethyl4-(1-(tert-butoxycarbonyl)piperidin-4-ylamino)-2-(2,2,2-trifluoroethyl)thieno[2,3-b]pyridine-5-carboxylate.To a solution of5-(ethoxycarbonyl)-2-(2,2,2-trifluoroethyl)thieno[2,3-b]pyridin-4-yltrifluoromethanesulfonate (108 mg, 0.25 mmol) in THF (2.5 mL) was addedN,N-diisopropylethylamine (69 uL, 0.40 mmol) and tert-butyl4-aminopiperidine-1-carboxylate (55 mg, 0.27 mmol). The solution washeated to 60° C. for 2 hours. The volatiles were removed in vacuo. Theresidue was dissolved in EtOAc (10 mL), washed subsequently with 0.1 NNaHSO₄ (2×5 mL) and saturated aq. NaHCO₃ (1×5 mL). The organic phase wasdried over Na₂SO₄ and evaporated in vacuo to give the product as a whitefoam (122 mg), which was used without further purification. LC-MS: 2.73min, 488.2 m/z [M+H]⁺, 432.1 m/z [M-t-Bu+H]⁺

Tert-butyl4-(2-(2,2,2-trifluoroethyl)-5-(hydroxymethyl)thieno[2,3-b]pyridin-4-ylamino)piperidine-1-carboxylate.Ethyl4-(1-(tert-butoxycarbonyl)piperidin-4-ylamino)-2-(2,2,2-trifluoroethyl)thieno[2,3-b]pyridine-5-carboxylate (122 mg, 0.25 mmol) was dissolved inTHF (2.0 mL). Lithium borohydride (0.5 mL, 2.0 M solution in THF, 1.0mmol) was added. The solution was heated to reflux under nitrogen for 1hour. After cooling to room temperature, water (1 mL) was carefullyadded to the mixture. The mixture was concentrated in vacuo. Methanol(10 mL) was added and the solution concentrated to dryness on a rotaryevaporator. The addition of methanol and evaporation was repeated threeadditional times. Purification of the resultant residue by silica gelchromatography (10:1 to 1:1 gradient of hexanes/EtOAc) afforded theproduct as a yellow solid (45 mg, 40% yield). LC-MS: 2.35 min, 446.3 m/z[M+H]⁺, 390.3 m/z [M-t-Bu+H]⁺

Ethyl4-(1-(tert-butoxycarbonyl)piperidin-4-ylamino)-2-(2,2,2-trifluoroethyl)thieno[2,3-b]pyridine-5-carboxylate(45 mg, 0.1 mmol) was dissolved in CH₂Cl₂ (3 mL). Trifluoroacetic acid(2 mL) was added to the solution. After 2 hours, the solution wasconcentrated in vacuo. The residue was dissolved in CH₂Cl₂ (10 mL), andwashed with a 10% solution of K₂CO₃ (2×1 mL), and dried over anhydrousK₂CO₃. The organic phase was concentrated to give tan residue, which wasused in the next step without further purification. This residue wasdissolved in 1,2-dichloroethane (1 mL).5-formyl-1H-indole-2-carbonitrile (23 mg, 0.14 mmol) and sodiumtri(acetoxy)borohydride (32 mg, 0.15 mmol) were added. The mixture wasstirred at room temperature for 2 hours. The solution was diluted withEtOAc (10 mL) and washed with 0.1 N NaOH (1×5 mL). The organic phase wasdried over Na₂SO₄ and concentrated in vacuo. The resulting residue waspurified by reversed-phase preparative HPLC (95:5-5:95 MeCN/H₂O with0.1% HCl buffer). The product containing fractions were lyophilized toafford the product as a white solid (1.4 mg, 2.5% yield), Compound 278.LC-MS: 1.45 min, 500.2 m/z [M+H]⁺.

Example 9 Fluorescence Polarization (FP) Assay

Fluorescence Polarization Assay.

Assays effective in monitoring the inhibition of the MLL binding tomenin were developed during experiments performed during the developmentof embodiments of the present invention. A fluorescein-labeled 12-aminoacid peptide derived from MLL containing the high affinity menin bindingmotif was produced (Yokoyama et al., Cell., 2005. 123(2): p. 207-18,herein incorporated by reference in its entirety). Upon binding of thepeptide (1.7 kDa) to the much larger menin (−67 kDa), the rotationalcorrelation time of the fluorophore (peptide labeled with fluorescein atN-terminus) changes significantly, resulting in a substantial increasein the measured fluorescence polarization and fluorescence anisotropy(excitation at 500 nm, emission at 525 nm). The fluorescencepolarization (FP) assay was utilized to determine the K_(d) for thebinding of menin and the MLL peptide using a serial dilution of meninand 50 nM fluorescein-labeled MLL peptide. The titration curvedemonstrates nanomolar affinity (K_(d)=56 nM) for the menin-MLLinteraction.

The effectiveness of compounds (IC₅₀ values) in inhibiting the menin-MLLinteraction was determined in the FP competition experiments. Compoundsthat inhibit the interaction decrease the fluorescence anisotropy whichis being used as a read-out for compound screening and for IC₅₀determination. For validation of the FP assay, a control competitionexperiment with unlabeled MLL peptide (no fluorescein attached) wasperformed. The competitive displacement of the fluorescein-labeled MLLpeptide from menin by unlabeled MLL peptide was monitored. Using thisassay, the IC₅₀ value for the MLL peptide with menin: IC₅₀=0.23 μM. Insome embodiments of the present invention, the same competition FP assayis used for screening compounds targeting menin and inhibiting themenin-MLL interaction.

Biological activity of menin-MLL inhibitors is demonstrated in FIGS.1-19. The IC₅₀ values shown in Tables 1-8 were measured using the abovefluorescence polarization (FP) assay.

What is claimed is:
 1. A composition comprising a compound having thestructure of one of:


2. The composition of claim 1, wherein the compound is selected fromcompounds 1-283.
 3. A method for the treatment of a disease or conditioncomprising: administering a composition of claim 1 to a subjectsuffering from said disease or condition.
 4. The method of claim 3,wherein said disease or condition comprises a leukemia, solid tumorcancer, or diabetes.
 5. The method of claim 4, wherein said leukemiacomprises AML or ALL.
 6. A method of inhibiting the interaction of MLLand menin comprising administering composition of claim 1 to said samplecomprising MLL and menin.